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Journal articles on the topic 'Planted motif search'
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PATHAK, SUDIPTA, SANGUTHEVAR RAJASEKARAN, and MARIUS NICOLAE. "EMS1: AN ELEGANT ALGORITHM FOR EDIT DISTANCE BASED MOTIF SEARCH." International Journal of Foundations of Computer Science 24, no. 04 (2013): 473–86. http://dx.doi.org/10.1142/s0129054113500159.
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Motifs are biologically significant patterns found in DNA/protein sequences. Given a set of biological sequences, the problem of identifying the motifs is very challenging. This problem has been well studied in computational biology. Identifying motifs through experimental processes is extremely expensive and time consuming. This is one of the factors influencing computational biologists to come up with novel computational methods to predict motifs. Several motif models have been proposed in the literature and for each model numerous algorithms have been devised. Three popular motif models are (l, d)-motif search or Planted Motif Search (PMS), Simple Motif Search (SMS), and Edit-distance based Motif Search (EMS). For PMS and SMS several algorithms have been proposed and implemented. On the other hand, even though some algorithms exist in the literature for the problem of EMS, no implementations of these algorithms are known. This is mainly because the proposed algorithms are complex. In this paper we present an elegant algorithm for EMS. We have implemented this algorithm and compared it against 14 other algorithms in terms of sensitivity and specificity. Our experimental results indicate that the new algorithm is very competitive in practice.
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ZHANG, YIPU, HONGWEI HUO, and QIANG YU. "A HEURISTIC CLUSTER-BASED EM ALGORITHM FOR THE PLANTED (l, d) PROBLEM." Journal of Bioinformatics and Computational Biology 11, no. 04 (2013): 1350009. http://dx.doi.org/10.1142/s0219720013500091.
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The planted motif search problem arises from locating the transcription factor binding sites (TFBSs) which are crucial for understanding the gene regulatory relationship. Many attempts in using expectation maximization for TFBSs discovery are successful in past. However, identifying highly degenerate motifs and reducing the effect of local optima are still an arduous task. To alleviate the vulnerability of EM to local optima trapping, we present a heuristic cluster-based EM algorithm, CEM, which refines the cluster subsets in EM method to explore the best local optimal solution. Based on experiments using both synthetic and real datasets, our algorithm demonstrates significant improvements in identifying the motif instances and performs better than current widely used algorithms. CEM is a novel planted motif finding algorithm, which is able to solve the challenging instances and easy to parallel since the process of solving each cluster subset is independent.
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Theepalakshmi, P., та U. Srinivasulu Reddy. "Freezing firefly algorithm for efficient planted (ℓ, d) motif search". Medical & Biological Engineering & Computing 60, № 2 (2022): 511–30. http://dx.doi.org/10.1007/s11517-021-02468-x.
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Davila, J., S. Balla, and S. Rajasekaran. "Fast and Practical Algorithms for Planted (l, d) Motif Search." IEEE/ACM Transactions on Computational Biology and Bioinformatics 4, no. 4 (2007): 544–52. http://dx.doi.org/10.1109/tcbb.2007.70241.
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Xu, Yun, Jiaoyun Yang, Yuzhong Zhao, and Yi Shang. "An improved voting algorithm for planted (l,d) motif search." Information Sciences 237 (July 2013): 305–12. http://dx.doi.org/10.1016/j.ins.2013.03.023.
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Lala, Septem Riza, Farrah Dhiba Tyas, Setiawan Wawan, Hidayat Topik, and Fahs Mahmoud. "Parallel random projection using R high performance computing for planted motif search." TELKOMNIKA Telecommunication, Computing, Electronics and Control 17, no. 3 (2019): 1352–59. https://doi.org/10.12928/TELKOMNIKA.v17i3.11750.
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Motif discovery in DNA sequences is one of the most important issues in bioinformatics. Thus, algorithms for dealing with the problem accurately and quickly have always been the goal of research in bioinformatics. Therefore, this study is intended to modify the random projection algorithm to be implemented on R high performance computing (i.e., the R package pbdMPI). Some steps are needed to achieve this objective, ie preprocessing data, splitting data according to number of batches, modifying and implementing random projection in the pbdMPI package, and then aggregating the results. To validate the proposed approach, some experiments have been conducted. Several benchmarking data were used in this study by sensitivity analysis on number of cores and batches. Experimental results show that computational cost can be reduced, which is that the computation cost of 6 cores is faster around 34 times compared with the standalone mode. Thus, the proposed approach can be used for motif discovery effectively and efficiently.
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Sun, Chunxiao, Hongwei Huo, Qiang Yu, Haitao Guo, and Zhigang Sun. "An Affinity Propagation-Based DNA Motif Discovery Algorithm." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/853461.
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The planted(l,d)motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.
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Xiao, Peng, Soumitra Pal, and Sanguthevar Rajasekaran. "Randomised sequential and parallel algorithms for efficient quorum planted motif search." International Journal of Data Mining and Bioinformatics 18, no. 2 (2017): 105. http://dx.doi.org/10.1504/ijdmb.2017.086457.
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Xiao, Peng, Soumitra Pal, and Sanguthevar Rajasekaran. "Randomised sequential and parallel algorithms for efficient quorum planted motif search." International Journal of Data Mining and Bioinformatics 18, no. 2 (2017): 105. http://dx.doi.org/10.1504/ijdmb.2017.10007475.
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Riza, Lala Septem, Tyas Farrah Dhiba, Wawan Setiawan, Topik Hidayat, and Mahmoud Fahsi. "Parallel random projection using R high performance computing for planted motif search." TELKOMNIKA (Telecommunication Computing Electronics and Control) 17, no. 3 (2019): 1352. http://dx.doi.org/10.12928/telkomnika.v17i3.11750.
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Tanaka, Shunji. "Improved Exact Enumerative Algorithms for the Planted ($l$, $d$)-Motif Search Problem." IEEE/ACM Transactions on Computational Biology and Bioinformatics 11, no. 2 (2014): 361–74. http://dx.doi.org/10.1109/tcbb.2014.2306842.
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Yu, Qiang, Hongwei Huo, Yipu Zhang, and Hongzhi Guo. "PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search." PLoS ONE 7, no. 10 (2012): e48442. http://dx.doi.org/10.1371/journal.pone.0048442.
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Yu, Qiang, and Xiao Zhang. "A New Efficient Algorithm for Quorum Planted Motif Search on Large DNA Datasets." IEEE Access 7 (2019): 129617–26. http://dx.doi.org/10.1109/access.2019.2940115.
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Kazemian, Fazeleh Sadat, Mahmood Fazlali, Ali Katanforoush та Mojtaba Rezvani. "Parallel implementation of quorum planted (ℓ, d ) motif search on multi-core/many-core platforms". Microprocessors and Microsystems 46 (жовтень 2016): 255–63. http://dx.doi.org/10.1016/j.micpro.2016.06.008.
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Teresinski, Howard J., Satinder K. Gidda, Thuy N. D. Nguyen, et al. "An RK/ST C-Terminal Motif is Required for Targeting of OEP7.2 and a Subset of Other Arabidopsis Tail-Anchored Proteins to the Plastid Outer Envelope Membrane." Plant and Cell Physiology 60, no. 3 (2018): 516–37. http://dx.doi.org/10.1093/pcp/pcy234.
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Abstract Tail-anchored (TA) proteins are a unique class of integral membrane proteins that possess a single C-terminal transmembrane domain and target post-translationally to the specific organelles at which they function. While significant advances have been made in recent years in elucidating the mechanisms and molecular targeting signals involved in the proper sorting of TA proteins, particularly to the endoplasmic reticulum and mitochondria, relatively little is known about the targeting of TA proteins to the plastid outer envelope. Here we show that several known or predicted plastid TA outer envelope proteins (OEPs) in Arabidopsis possess a C-terminal RK/ST sequence motif that serves as a conserved element of their plastid targeting signal. Evidence for this conclusion comes primarily from experiments with OEP7.2, which is a member of the Arabidopsis 7 kDa OEP family. We confirmed that OEP7.2 is localized to the plastid outer envelope and possesses a TA topology, and its C-terminal sequence (CTS), which includes the RK/ST motif, is essential for proper targeting to plastids. The CTS of OEP7.2 is functionally interchangeable with the CTSs of other TA OEPs that possess similar RK/ST motifs, but not with those that lack the motif. Further, a bioinformatics search based on a consensus sequence led to the identification of several new OEP TA proteins. Collectively, this study provides new insight into the mechanisms of TA protein sorting in plant cells, defines a new targeting signal element for a subset of TA OEPs and expands the number and repertoire of TA proteins at the plastid outer envelope.
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Cooley, Sarah, Lisbeth Guethlein, Elizabeth Trachtenberg, et al. "Selection of Donors with Favorable KIR B Genotypes for Unrelated Hematopoietic Cell Transplantation Results in Superior Relapse Protection and Better Relapse-Free Survival for Patients with AML." Blood 114, no. 22 (2009): 665. http://dx.doi.org/10.1182/blood.v114.22.665.665.
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Abstract Abstract 665 Unrelated donor (URD) transplants from donors with KIR group B/x genotypes (vs. A/A) confer a significant relapse-free survival (RFS) benefit for patients with acute myeloid leukemia (AML) (RR: 0.70 [95% CI: 0.55-0.88]; P = .002; Blood 2009; 113[3]). This new analysis was designed to investigate the beneficial effect of KIR B donors and to develop a donor selection strategy to improve clinical outcomes after hematopoietic cell transplantation (HCT) for leukemia. Based on an analysis of 27 unique KIR haplotype sequences we identified common centromeric and telomeric gene content motifs. KIR A haplotypes contain a Cen-A motif (defined by the presence of the inhibitory KIR gene 2DL3) and a Tel-A motif (defined by the presence of the activating gene 2DS4). The B haplotypes were defined as containing Cen-B (presence of 2DS2 and/or 2DL2) and/or Tel-B (presence of 2DS1), with further subdivisions possible at the allelic level. Thus, based on gene content alone, donor KIR genotypes can be classified as homogyzous A/A or defined by the type (Cen-B or Tel-B) or number (0, 1, 2 or ≥3; B domain content score) of B domains. Multivariate models were used to evaluate the effect of donor KIR genotypes on clinical outcomes after URD transplants facilitated by the National Marrow Donor Program for AML (n=1086) and acute lymphoblastic leukemia (ALL: n=334) between 1988 and 2006. The improved RFS associated with donor KIR B genotypes (Cen-A/B, Cen-B/B, Tel-A/B or Tel-B/B) vs. KIR A genotypes (Cen-A/A or Tel-A/A) in AML was most evident in the 115 donors (10.6%) who were homogyzous for the Cen-B motif (RR 0.72 [95% CI 0.55-0.94]; p=0.014). Likewise, Cen-B/B donors conferred significant protection against relapse (RR 0.34 [95% CI 0.2-0.57]; p < 0.0001); with absolute relapse rates of only 10% (Cen-B/B) vs. ∼31% (A/A). Similarly, multivariate models demonstrated that compared to KIR A/A donors, donors with higher KIR B domain content scores resulted in improved RFS (2B motifs: (RR 0.78 [95% CI 0.63-0.95]; p=0.013; n=244) or ≥3 B motifs: (RR 0.76 [95% CI 0.57-1.02]; p=0.07; n=84) and less relapse (2B motifs: (RR 0.54 [95% CI 0.39-0.74]; p=0.0001) or ≥3 B motifs: (RR 0.45 [95% CI 0.27-0.74]; p=0.0017). Donor KIR genotype had no effect on rates of graft vs. host disease or treatment related mortality. Importantly, the use of KIR B donors of any type was not associated with any improvement in clinical outcomes for patients with ALL. These data suggest that AML blasts may be particularly sensitive to killing by NK cells and raises the possibility that activating genes present in the donor KIR B haplotypes may uniquely recognize ligands on AML blasts. The KIR B genotype effects were not affected by the degree of HLA matching. Therefore, these data support the consideration of KIR genotyping with HLA typing into the unrelated donor search criteria for patients with AML. To capture the benefit of Cen-B and/or higher B domain content scores we propose that the ∼30% of donors who have ≥2 B domains (includes all Cen-B/B donors) be given preference over donors with 0 or 1 KIR B domains. In this large retrospective dataset, assignment by that rule resulted in significant improvements in RFS (RR 0.80 [95% CI 0.68-0.94]; p=0.0063) and relapse (RR 0.53 [95% CI 0.41-0.69]; p<0.0001). A prospective trial to test this strategy is planned. Disclosures: No relevant conflicts of interest to declare.
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Zaynab, Madiha, Athar Hussain, Yasir Sharif, et al. "Mitogen-Activated Protein Kinase Expression Profiling Revealed Its Role in Regulating Stress Responses in Potato (Solanum tuberosum)." Plants 10, no. 7 (2021): 1371. http://dx.doi.org/10.3390/plants10071371.
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Mitogen-activated protein kinase (MAPK) cascades are the universal signal transduction networks that regulate cell growth and development, hormone signaling, and other environmental stresses. However, their essential contribution to plant tolerance is very little known in the potato (Solanum tuberosum) plant. The current study carried out a genome-wide study of StMAPK and provided a deep insight using bioinformatics tools. In addition, the relative expression of StMAPKs was also assessed in different plant tissues. The similarity search results identified a total of 22 StMAPK genes in the potato genome. The sequence alignment also showed conserved motif TEY/TDY in most StMAPKs with conserved docking LHDXXEP sites. The phylogenetic analysis divided all 22 StMAPK genes into five groups, i.e., A, B, C, D, and E, showing some common structural motifs. In addition, most of the StMAPKs were found in a cluster form at the terminal of chromosomes. The promoter analysis predicted several stress-responsive Cis-acting regulatory elements in StMAPK genes. Gene duplication under selection pressure also indicated several purifying and positive selections in StMAPK genes. In potato, StMAPK2, StMAPK6, and StMAPK19 showed a high expression in response to heat stress. Under ABA and IAA treatment, the expression of the total 20 StMAPK genes revealed that ABA and IAA played an essential role in this defense process. The expression profiling and real-time qPCR (RT-qPCR) exhibited their high expression in roots and stems compared to leaves. These results deliver primary data for functional analysis and provide reference data for other important crops.
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Lessa, Renato Corrêa da Silva. "Synthetic Organic Molecules as Metallic Corrosion Inhibitors: General Aspects and Trends." Organics 4, no. 2 (2023): 232–50. http://dx.doi.org/10.3390/org4020019.
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Organic molecules are gaining special attention over the last years in the corrosion area thanks to their general low achievable cytotoxicity, structural versatility, and environmentally friendly obtainment methods. Under those approaches, synthetic organic motifs have attracted the interest of researchers due to their variated methods of obtention through molecular manipulation via diverse chemical reactions, allowing the production of adequately planned structures or repurposing their original application in the case of drugs. This review summarizes general aspects that are desired in organic molecules as corrosion inhibitors, presenting selected works published in the 2022–2023 period and emphasizing the importance of finding novel and different organic corrosion inhibitors. Patents were not considered in this review. Scifinder, Google Scholar, and Web of Science were employed as databases. Mathematical and analytical methods involved in the search for corrosion inhibitors are out of this review’s scope.
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Beauchet, Arthur, Frédéric Gévaudant, Nathalie Gonzalez, and Christian Chevalier. "In search of the still unknown function of FW2.2/CELL NUMBER REGULATOR, a major regulator of fruit size in tomato." Journal of Experimental Botany 72, no. 15 (2021): 5300–5311. http://dx.doi.org/10.1093/jxb/erab207.
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Abstract The FW2.2 gene is associated with the major quantitative trait locus (QTL) governing fruit size in tomato, and acts by negatively controlling cell division during fruit development. FW2.2 belongs to a multigene family named the CELL NUMBER REGULATOR (CNR) family. CNR proteins harbour the uncharacterized PLAC8 motif made of two conserved cysteine-rich domains separated by a variable region that are predicted to be transmembrane segments, and indeed FW2.2 localizes to the plasma membrane. Although FW2.2 was cloned more than two decades ago, the molecular mechanisms of action remain unknown. In particular, how FW2.2 functions to regulate cell cycle and fruit growth, and thus fruit size, is as yet not understood. Here we review current knowledge on PLAC8-containing CNR/FWL proteins in plants, which are described to participate in organogenesis and the regulation of organ size, especially in fruits, and in cadmium resistance, ion homeostasis, and/or Ca2+ signalling. Within the plasma membrane FW2.2 and some CNR/FWLs are localized in microdomains, which is supported by recent data from interactomics studies. Hence FW2.2 and CNR/FWL could be involved in a transport function of signalling molecules across membranes, influencing organ growth via a cell to cell trafficking mechanism.
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Reingold, Victoria, Avi Eliyahu, Neta Luria, et al. "A Distinct Arabidopsis Latent Virus 1 Isolate Was Found in Wild Brassica hirta Plants and Bees, Suggesting the Potential Involvement of Pollinators in Virus Spread." Plants 13, no. 5 (2024): 671. http://dx.doi.org/10.3390/plants13050671.
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During our search for aphid-pathogenic viruses, a comovirus was isolated from wild asymptomatic Brassica hirta (white mustard) plants harboring a dense population of Brevicoryne brassicae aphids. The transmission-electron-microscopy visualization of purified virions revealed icosahedral particles. The virus was mechanically transmitted to plants belonging to Brassicaceae, Solanaceae, Amaranthaceae, and Fabaceae families, showing unique ringspot symptoms only on B. rapa var. perviridis plants. The complete viral genome, comprised of two RNA segments, was sequenced. RNA1 and RNA2 contained 5921 and 3457 nucleotides, respectively, excluding the 3′ terminal poly-adenylated tails. RNA1 and RNA2 each had one open-reading frame encoding a polyprotein of 1850 and 1050 amino acids, respectively. The deduced amino acids at the Pro-Pol region, delineated between a conserved CG motif of 3C-like proteinase and a GDD motif of RNA-dependent RNA polymerase, shared a 96.5% and 90% identity with the newly identified Apis mellifera-associated comovirus and Arabidopsis latent virus 1 (ArLV1), respectively. Because ArLV1 was identified early in 2018, the B. hirta comovirus was designated as ArLV1-IL-Bh. A high-throughput-sequencing-analyses of the extracted RNA from managed honeybees and three abundant wild bee genera, mining bees, long-horned bees, and masked bees, sampled while co-foraging in a Mediterranean ecosystem, allowed the assembly of ArLV1-IL-Bh, suggesting pollinators’ involvement in comovirus spread in weeds.
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Amaral, Paulo de Paiva Rosa, Paulo César Martins Alves, Natália Florêncio Martins, Felipe Rodrigues da Silva, Guy de Capdeville, and Manoel Teixeira Souza Júnior. "Identification and characterization of a resistance gene analog (RGA) from the Caricaceae Dumort family." Revista Brasileira de Fruticultura 28, no. 3 (2006): 458–62. http://dx.doi.org/10.1590/s0100-29452006000300026.
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The majority of cloned resistance (R) genes characterized so far contain a nucleotide-binding site (NBS) and a leucine-rich repeat (LRR) domain, where highly conserved motifs are found. Resistance genes analogs (RGAs) are genetic markers obtained by a PCR-based strategy using degenerated oligonucleotide primers drawn from these highly conserved "motifs". This strategy has the advantage of the high degree of structural and amino acid sequence conservation that is observed in R genes. The objective of the present study was to search for RGAs in Carica papaya L. and Vasconcellea cauliflora Jacq. A. DC. Out of three combinations of primers tested, only one resulted in amplification. The amplified product was cloned in pCR2.1TOPO and than sequenced using M13 forward and reverse primers. Forty-eight clones were sequenced from each species. The 96 sequences generated for each species were cleaned of vector sequences and clustered using CAP3 assembler. From the GENEBANK, one RGA was identified in C. papaya showing a BlastX e-value of 2x10-61 to the gb|AAP45165.1| putative disease resistant protein RGA3 (Solanum bulbocastanum). To the extent of our knowledge this is the first report of a RGA in the Caricaceae Dumort family. Preliminary structural studies were performed to further characterize this putative NBS-LRR type protein. Efforts to search for other RGAs in papaya should continue, mostly to provide basis for the development of transgenic papaya with resistance to diseases.
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Khan, Afiqah, Nor Mokthar, Zarina Zainuddin, and Nurul Samsulrizal. "In silico Characterization of UGT74G1 Protein in Stevia rebaudiana Bertoni Accession MS007." Journal of Tropical Life Science 11, no. 3 (2021): 323–30. http://dx.doi.org/10.11594/jtls.11.03.09.
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Due to its low-calorie property, Stevia rebaudiana is being promoted as an alternative sweetener for diabetic and obese patients. The steady demand in the market for high-quality stevia extracts presents a challenge for the enhanced production of steviol glycosides that are safe for human consumption. This study characterized the structure and content of the gene involved in the production of UGT74G1 protein for Stevia rebaudiana accession MS007 through in silico analysis using a transcriptome dataset of stevia MS007. Homologous search using BLASTp shows high similarity to Q6VAA6 RecName: Full=UDP-glycosyltransferase 74G1 (S. rebaudiana) as the top hit sequence. InterPro family and domain protein motif search revealed UDP-glucuronosyl/UDP-glucosyltransferase (IPR002213) and UDP-glycosyltransferase family, conserved site (IPR035595). The phylogenetic tree construction was done by selecting 14 out of 102 protein sequences from BLASTp search. The phylogenetic analysis revealed a high value of bootstrapping, which was 100, indicating the high similarity between UGT74G1 (Q6VAA6.1 and Cluster-31069.45201) in S. rebaudiana. ProtParam ExPASy, PSIPRED, and Phyre2 computed the primary, secondary, and tertiary structures for UGT74G1 protein. The UGT74G1 predicted tertiary structure scored 100.0% confidence by the single highest scoring template and coverage of 96%. The model has dimensions (Å) of X: 57.609, Y: 70.386, and Z: 58.351. Outcomes of this research will help enhance understanding UDP-glycosyltransferase 74G1 (S. rebaudiana MS007) characteristics and enhance target identification processes to improve understanding of protein-protein interaction in S. rebaudiana MS007.
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Ma, Biao, Lili Nian, Noor ul Ain, et al. "Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions." Plants 11, no. 22 (2022): 3101. http://dx.doi.org/10.3390/plants11223101.
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The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.
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Liu, Xiaojuan, Ziquan Zhao, Yingying Yang, Huihui Xu, Quanxin Bi, and Libing Wang. "Genome-Wide Identification and Expression Analysis of the KCS Gene Family in Yellow Horn Reveal Their Putative Function on Abiotic Stress Responses and Wax Accumulation." Horticulturae 9, no. 1 (2022): 25. http://dx.doi.org/10.3390/horticulturae9010025.
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The β-ketoacyl CoA synthase encoded by the KCS genes is a rate-limiting enzyme for the synthesis of very-long-chain fatty acid (VLCFA), which catalyzes the VLCFA elongation. Yellow horn (Xanthoceras sorbifolium) is a horticultural tree species known for its kernel oil, which has strong resistance to drought, cold, high temperature, and saline-alkali. The conserved domain FAE1-CUT1-RPPA and ACP-syn-III_C of the KCS gene family were used to search the KCS sequences across the whole genomic sequence of yellow horn; a total of 20 XsKCS genes were identified and divided into four subfamilies. The conserved motif and transmembrane structure analysis revealed that most XsKCSs had a conserved transmembrane domain except XsKCS10 and XsKCS20. The prediction of cis-acting elements of XsKCS genes showed that XsKCS genes contained many stress and hormone response elements, such as ABRE, MBS, and LTR. Furthermore, XsKCS genes exhibited differential expression profiles under abiotic stress and stress-related hormone treatment conditions. Transcriptomic data showed that XsKCS1, XsKCS11, and XsKCS17 had higher expression in yellow horn with high leaf cuticular wax, indicating that they may function in the cuticular wax accumulation and drought response. This study laid a foundation for further functional verification of XsKCS genes in yellow horn stress response.
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Li, Zhidong, Ying Li, Tongkun Liu, Changwei Zhang, Dong Xiao, and Xilin Hou. "Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis." Plants 11, no. 8 (2022): 1005. http://dx.doi.org/10.3390/plants11081005.
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The availability of a high-quality genome sequence of Brassica campestris ssp. chinensis NHCC001 has paved the way for deep mining of genome data. We used the B. campestris NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the B. campestris NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding.
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Liu, Chan, Qing Tang, Chaohua Cheng, et al. "Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou." Plant Genetic Resources: Characterization and Utilization 16, no. 4 (2018): 306–14. http://dx.doi.org/10.1017/s1479262117000338.
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AbstractChinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.
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Zhang, Lingchao, Bobo Song, Bo Li, et al. "Genome-Wide Identification and Expression Analysis of Fifteen Gene Families Involved in Anthocyanin Synthesis in Pear." Horticulturae 10, no. 4 (2024): 335. http://dx.doi.org/10.3390/horticulturae10040335.
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Anthocyanins play a crucial role in imparting red coloration to pear fruits. However, the specific number and expression patterns of each member within the anthocyanin biosynthesis-related gene families in pears require systematic exploration. In this study, based on the pear genome we identified 15 gene families involved in the anthocyanin biosynthesis pathway using the BLASTP and Hidden Markov Model search methods, comprising a total of 94 enzyme genes. Through phylogenetic analysis, conserved domains, motif, and gene structure analysis, these gene families were further categorized into eight distinct lineages. Subsequent collinearity analysis revealed that the expansion of anthocyanin synthesis-related gene families primarily originated from segmental duplications. Analysis of cis-element in the promoter regions of genes related to anthocyanin synthesis unveiled the presence of light-responsive elements and various hormone-responsive elements. This suggests that changes in light stimulation and hormone levels may influence anthocyanin synthesis. RNA-Seq and qRT-PCR analyses indicated differential expression of anthocyanin biosynthesis-related genes between the peel and flesh tissues. During the accumulation of anthocyanins in red-fleshed pears, upstream genes in the anthocyanin biosynthesis pathway such as PbrPAL2, PbrC4H2, PbrC4H3, Pbr4CL2, Pbr4CL17, PbrF3H5, and PbrF3H6 exhibited high expression levels, likely contributing significantly to the red coloration of pear flesh. In summary, we have identified the number of gene family members involved in pear anthocyanin biosynthesis and analyzed the expression patterns of the genes related to pear anthocyanin biosynthesis. These findings provide a solid foundation for further research on the regulatory mechanisms underlying pear anthocyanin biosynthesis and the breeding of red pear varieties.
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Li, Yilin, Mengying Ding, Chuang Cui, et al. "Overexpression of a Gene Encoding Trigonelline Synthase from Areca catechu L. Promotes Drought Resilience in Transgenic Arabidopsis." Plants 11, no. 4 (2022): 487. http://dx.doi.org/10.3390/plants11040487.
Full textAbstract:
Areca catechu L. is a commercially important palm tree widely cultured in tropical and subtropical areas. Its growth and production are severely hindered by the increasing threat of drought. In the present study, we investigated the physiological responses of areca seedlings to drought stress. The results showed that prolonged drought-induced yellowing on the overall area of most leaves significantly altered the chlorophyll fluorescence parameters, including maximum chemical efficiency (Fv/Fm), photochemical efficiency of PSII (Y(II)), photochemical chlorophyll fluorescence quenching (qP) and non-photochemical chlorophyll fluorescence quenching (NPQ). On the 10th day of drought treatment, the contents of proline in the areca leaves and roots increased, respectively, by 12.2 times and 8.4 times compared to normal watering. The trigonelline levels in the leaves rose from 695.35 µg/g to 1125.21 µg/g under 10 days of water shortage, while no significant changes were detected in the content of trigonelline in the roots. We determined the gene encoding areca trigonelline synthase (AcTS) by conducting a bioinformatic search of the areca genome database. Sequence analysis revealed that AcTS is highly homologous to the trigonelline synthases in Coffea arabica (CaTS 1 and CaTS 2) and all possess a conserved S-adenosyl- L-methionine binding motif. The overexpression of AcTS in Arabidopsis thaliana demonstrated that AcTS is responsible for the generation of trigonelline in transgenic Arabidopsis, which in turn improves the drought resilience of transgenic Arabidopsis. This finding enriches our understanding of the molecular regulatory mechanism of the response of areca to water shortage and provides a foundation for improving the drought tolerance of areca seedlings.
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Soren, Khela Ram, Aravind Kumar Konda, Priyanka Gangwar, et al. "Development of SSR markers and association studies of markers with phenology and yield-related traits in grass pea (Lathyrus sativus)." Crop and Pasture Science 71, no. 8 (2020): 768. http://dx.doi.org/10.1071/cp19557.
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Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.
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Hua, Huihui, Xinyi Zhang, Jie Xia, and Xuehong Wu. "A Novel Strain of Fusarium oxysporum Virus 1 Isolated from Fusarium oxysporum f. sp. niveum Strain X-GS16 Influences Phenotypes of F. oxysporum Strain HB-TS-YT-1hyg." Journal of Fungi 10, no. 4 (2024): 252. http://dx.doi.org/10.3390/jof10040252.
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A novel strain of Fusarium oxysporum virus 1 (FoV1) was identified from the Fusarium oxysporum f. sp. niveum strain X-GS16 and designated as Fusarium oxysporum virus 1-FON (FoV1-FON). The full genome of FoV1-FON is 2902 bp in length and contains two non-overlapping open reading frames (ORFs), ORF1 and ORF2, encoding a protein with an unknown function (containing a typical −1 slippery motif G_GAU_UUU at the 3′-end) and a putative RNA-dependent RNA polymerase (RdRp), respectively. BLASTx search against the National Center for the Biotechnology Information (NCBI) non-redundant database showed that FoV1-FON had the highest identity (97.46%) with FoV1. Phylogenetic analysis further confirmed that FoV1-FON clustered with FoV1 in the proposed genus Unirnavirus. FoV1-FON could vertically transmit via spores. Moreover, FoV1-FON was transmitted horizontally from the F. oxysporum f. sp. niveum strain X-GS16 to the F. oxysporum strain HB-TS-YT-1hyg. This resulted in the acquisition of the F. oxysporum strain HB-TS-YT-1hyg-V carrying FoV1-FON. No significant differences were observed in the sporulation and dry weight of mycelial biomass between HB-TS-YT-1hyg and HB-TS-YT-1hyg-V. FoV1-FON infection significantly increased the mycelial growth of HB-TS-YT-1hyg, but decreased its virulence to potato tubers and sensitivity to difenoconazole, prochloraz, and pydiflumetofen. To our knowledge, this is the first report of hypovirulence and reduced sensitivity to difenoconazole, prochloraz, and pydiflumetofen in F. oxysporum due to FoV1-FON infection.
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León-García, Fabiola, Federico García-Laynes, Georgina Estrada-Tapia, Miriam Monforte-González, Manuel Martínez-Estevez, and Ileana Echevarría-Machado. "In Silico Analysis of Glutamate Receptors in Capsicum chinense: Structure, Evolution, and Molecular Interactions." Plants 13, no. 6 (2024): 812. http://dx.doi.org/10.3390/plants13060812.
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Plant glutamate receptors (GLRs) are integral membrane proteins that function as non-selective cation channels, involved in the regulation of developmental events crucial in plants. Knowledge of these proteins is restricted to a few species and their true agonists are still unknown in plants. Using tomato SlGLRs, a search was performed in the pepper database to identify GLR sequences in habanero pepper (Capsicum chinense Jacq.). Structural, phylogenetic, and orthology analysis of the CcGLRs, as well as molecular docking and protein interaction networks, were conducted. Seventeen CcGLRs were identified, which contained the characteristic domains of GLR. The variation of conserved residues in the M2 transmembrane domain between members suggests a difference in ion selectivity and/or conduction. Also, new conserved motifs in the ligand-binding regions are reported. Duplication events seem to drive the expansion of the species, and these were located in the evolution by using orthologs. Molecular docking analysis allowed us to identify differences in the agonist binding pocket between CcGLRs, which suggest the existence of different affinities for amino acids. The possible interaction of some CcGLRs with proteins leads to suggesting specific functions for them within the plant. These results offer important functional clues for CcGLR, probably extrapolated to other Solanaceae.
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Agrawal, Shivankar, Pruthviraj Chavan, and Laurent Dufossé. "Hidden Treasure: Halophilic Fungi as a Repository of Bioactive Lead Compounds." Journal of Fungi 10, no. 4 (2024): 290. http://dx.doi.org/10.3390/jof10040290.
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The pressing demand for novel compounds to address contemporary health challenges has prompted researchers to venture into uncharted territory, including extreme ecosystems, in search of new natural pharmaceuticals. Fungi capable of tolerating extreme conditions, known as extremophilic fungi, have garnered attention for their ability to produce unique secondary metabolites crucial for defense and communication, some of which exhibit promising clinical significance. Among these, halophilic fungi thriving in high-salinity environments have particularly piqued interest for their production of bioactive molecules. This review highlights the recent discoveries regarding novel compounds from halotolerant fungal strains isolated from various saline habitats. From diverse fungal species including Aspergillus, Penicillium, Alternaria, Myrothecium, and Cladosporium, a plethora of intriguing molecules have been elucidated, showcasing diverse chemical structures and bioactivity. These compounds exhibit cytotoxicity against cancer cell lines such as A549, HL60, and K-562, antimicrobial activity against pathogens like Escherichia coli, Bacillus subtilis, and Candida albicans, as well as radical-scavenging properties. Notable examples include variecolorins, sclerotides, alternarosides, and chrysogesides, among others. Additionally, several compounds display unique structural motifs, such as spiro-anthronopyranoid diketopiperazines and pentacyclic triterpenoids. The results emphasize the significant promise of halotolerant fungi in providing bioactive compounds for pharmaceutical, agricultural, and biotechnological uses. However, despite their potential, halophilic fungi are still largely unexplored as sources of valuable compounds.
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von Bargen, S., T. Büttner, H. P. Mühlbach, J. Robel, and C. Büttner. "First Report of European mountain ash ringspot-associated virus in Sorbus aucuparia in Norway." Plant Disease 98, no. 5 (2014): 700. http://dx.doi.org/10.1094/pdis-09-13-0955-pdn.
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In July 2012, leaf mottle and intensive chlorotic ringspots were observed on urban, forest, or roadside mountain ash trees (Sorbus aucuparia L., rowan) of different ages in Norway during visual inspection of native broadleaf forest tree species. Symptoms resembled those caused by European mountain ash ringspot-associated virus (EMARaV), the type-member of the newly established genus Emaravirus, containing segmented ss(-)RNA and infecting woody host species (2). Leaves of nine out of 30 assessed rowan trees exhibiting characteristic symptoms were sampled in the counties of Nordland and Nord-Trøndelag (between 63.511806° and 66.304680°N latitude). Three of them were infested by the potential vector the eriophyid gall mite Phytoptus pyri. EMARaV was detected from total RNA extracts of leaves by reverse transcription-PCR using virus-specific primers amplifying 300 bp of RNA2 and 204 bp of RNA3, respectively (3). PCR fragments were directly sequenced from both ends and submitted to the EMBL database (accession nos. HG428680 to 97). Sequenced fragments comprising the partial gene encoding the glycoprotein-precursor (261 nucleotides of RNA2 omitting primer sequences) obtained from the nine sampled trees showed identities of 97 to 98% to the sequence of the reference strain of EMARaV from Hamburg, Germany (database accession AY563041). Comparison of 159 nucleotides of the 3′ untranslated region (3′ UTR) of viral RNA3 of the nine investigated rowans in Norway exhibited higher sequence diversity on nucleotide level (up to 50 nucleotide exchanges, or 31%) as previously reported from EMARaV variants from other European countries (4). When subjected to BLASTn search through GenBank, only three partial RNA3 sequences generated in this study showed sequence identities of 96% to the reference isolate (accession DQ831831). The other six sequences revealed only 68 to 73% identity to RNA3 sequences of EMARaV variants from GenBank. This led to formation of a separate cluster in phylogenetic analysis of partial RNA3 sequences of the six EMARaV variants from Norway when compared to previously characterized strains from the Czech Republic (n = 2), Finland (n = 17), Germany (n = 1), Great Britain (n = 5), Russia (n = 3), and Sweden (n = 10). From three Norwegian samples clustering separately in the tree based on the partial 3′ UTR of RNA3, the partial vRNA1 was amplified by RT-PCR using a generic primer set Motif-A-sense/Motif-C-antisense (1). Sequence analyses of these PCR fragments confirmed the viruses as members of the Emaravirus genus which were most closely related to EMARaV (data not shown). This is the first report of EMARaV in Norway infecting Sorbus aucuparia, a valuable native plant of northern Europe. The data obtained suggest a higher genetic variability of the EMARaV population in mountain ash trees in Norway than in other locations in Central and Northern Europe. However, whether the EMARaV variants identified in this study represent new strains of the virus have to be investigated in the future. References: (1) T. Elbeaino et al. J. Virol. Meth. 188:37, 2013. (2) N. Mielke-Ehret. and H. P. Mühlbach. Viruses 4:1515, 2012. (3) N. Mielke et al. For. Pathol. 38:371, 2008. (4) S. von Bargen et al. For. Pathol. 43: 429, 2013.
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Vangelisti, Alberto, Samuel Simoni, Gabriele Usai, et al. "In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.)." Plants 11, no. 5 (2022): 664. http://dx.doi.org/10.3390/plants11050664.
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The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range of functions; these proteins have not been characterised in sunflower at the genomic level. In this work, we exploited the reliable genome sequence of sunflower to identify and characterise the LTP multigenic family in H. annuus. Overall, 101 sunflower putative LTP genes were identified using a homology search and the HMM algorithm. The selected sequences were characterised through phylogenetic analysis, exon–intron organisation, and protein structural motifs. Sunflower LTPs were subdivided into four clades, reflecting their genomic and structural organisation. This gene family was further investigated by analysing the possible duplication origin of genes, which showed the prevalence of tandem and whole genome duplication events, a result that is in line with polyploidisation events that occurred during sunflower genome evolution. Furthermore, LTP gene expression was evaluated on cDNA libraries constructed on six sunflower tissues (leaf, root, ligule, seed, stamen, and pistil) and from roots treated with stimuli mimicking biotic and abiotic stress. Genes encoding LTPs belonging to three out of four clades responded specifically to external stimuli, especially to abscisic acid, auxin, and the saline environment. Interestingly, genes encoding proteins belonging to one clade were expressed exclusively in sunflower seeds. This work is a first attempt of genome-wide identification and characterisation of the LTP multigenic family in a plant species.
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YINXIA, Wang, Ji XIANGZHUO, Zhuang ZELONG, Zhang YUNFANG, and Peng YUNLING. "Identification and bioinformatics analysis of MADS-box family genes containing K-box domain in maize." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 51, no. 4 (2023): 13253. http://dx.doi.org/10.15835/nbha51413253.
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The MADS-box family genes are involved in the development of plant roots, leaves, flowers, and fruits, and play a crucial role in plant growth and development. Studying MADS-box genes with K-box domain is crucial to distinguish different types of MADS-box genes. This study systematically analysed the genomic structural information of maize MADS-box family members containing the K-box Domain at the genome-wide level using the maize (Zea mays) B73 genome as the reference sequence, and provided insight into the biological functions of the maize MADS-box family containing the K-box domain. According to the findings, 52 MADS-box family genes with K-box domain were identified and divided into 4 subgroups. The distribution of motif in the same subgroup was found to be relatively conservative, and all of them had MADS-box conserved domain and K-box domain. Gene structure analysis showed that the introns and exons of the same subgroup genes have similar gene structure, and different types of genes containing the K-box domain showed different exon/intron structure characteristics. Chromosome mapping showed that 52 genes containing the K-box domain were unevenly distributed on the 10 chromosomes of maize, most of which were distributed at both ends of the chromosome and a small number of genes were distributed near the centromere. Based on the analysis of cis-acting elements of it up-stream promoter, it was found that MADS-box family genes may be involved in light response, IAA, GA, ABA, and LTR signal pathways, indicating that they play a certain role in stress response and hormone signal transduction. The expression analysis of genes with the K-box domain in maize leaves treated with auxin and gibberellin revealed that MADS-box genes may have a regulatory effect on certain plant hormones. Through the identification and bioinformatics analysis of MADS-box family genes containing the K-box domain, it is helpful to further study the function and pathway of MADS-box family genes, and provide a theoretical basis for further re-search for the molecular mechanism of maize growth and development.
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ANDRADE, Carlos G., Emanuel M. Da SILVA, Carla RAGONEZI, and Miguel Â. A. PINHEIRO DE CARVALHO. "Viral diagnosis in cultivars of Ipomoea batatas (L.) Lam." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 49, no. 1 (2021): 12222. http://dx.doi.org/10.15835/nbha49112222.
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Ipomoea batatas (L.) Lam. commonly known as sweet potato, is an important staple food worldwide, mainly due to its high nutritional value and yield. However, vegetative reproduction of sweet potato makes it more susceptible to viral infections, which threatens its productivity, quality, and difficult long-term preservation in germplasm banks. Also, it can act as a virus reservoir infecting the rest of the plant accessions in the bank collections. Hence, this work aimed to screen Begomovirus, Potyvirus, and Carlavirus infections in 16 traditional sweet potato cultivars from the germplasm collection of the ISOPlexis Germplasm Bank, Madeira, Portugal. The infection prevalence by these viruses among cultivars was 81.25%, 25.00%, and 6.25%, respectively; being ISOP1011 the only accession coinfected by Potyvirus and Carlavirus. The accessions ISOP1006, ISOP1010, and ISOP1047 were also coinfected by Begomovirus and Potyvirus, highlighting their vulnerability to viral infections. The ISOP1005 and ISOP1027 accessions were the only ones not infected by any of these viruses. The analysis of the partial sequence obtained from the Carlavirus detected in the accession ISOP1011, revealed the existence of an ORF that encodes for 93 amino acids of the catalytic domain of an RNA-directed RNA polymerase related to the Tymovirus protein family, as could be confirmed by comparison with proteins stored in UniProtKB. Multiple sequence alignment with these proteins showed that Motifs A and B of the catalytic domain were conserved. The search for sequence similarity with sequences deposited in GenBank reported a high sequence identity with Sweet potato yellow mottle virus (SPYMV) and Sweet potato chlorotic fleck virus (SPCFV). However, the 9-11% discrepancy in nucleotide sequence identity and a phylogenetic analysis carried out using the maximum probability method suggests the virus isolated from ISOP1011 is a new divergent strain of the SPCFV species.
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Idris, A. M., and J. K. Brown. "Three Previously Unidentified Begomoviral Genotypes from Tomato Exhibiting Leaf Curl Disease Symptoms from Central Sudan." Plant Disease 85, no. 11 (2001): 1209. http://dx.doi.org/10.1094/pdis.2001.85.11.1209a.
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Field tomato plants exhibiting upward curling of leaflets, chlorosis, and stunting symptoms described for tomato leaf curl disease in Sudan (2) were collected in 1996 from Gezira (GZ) and Shambat (SH), Sudan. Disease symptoms were reproduced following experimental transmission of the causal agent(s) by the whitefly Bemisia tabaci from field tomato to virus-free tomato seedlings in a glasshouse at Gezira Research Station, Wad Medani, Sudan. Total nucleic acids were extracted from symptomatic tomato test plants. An ≈1.3-kbp fragment, diagnostic for begomovirus, was obtained from extracts by polymerase chain reaction using degenerate primers that amplify the coat protein gene (CP) and the respective flanking sequences for most begomoviuses (1). A second pair of degenerate primers was used to amplify a 2.3-kbp begomoviral fragment that overlaps both ends of the (CP) amplicon by >200 nt (1). At least 10 amplicons for each were cloned, and their sequences were determined, revealing three unique, tomato-infecting begomoviruses genotypes, two from GZ and one from SH. No B component was detected using degenerate primers that direct the amplification of a diagnostic fragment of the B component (1.4 kbp) for most bipartite begomoviruses. The organization of the three, apparently full-length viral genomes, was typical of other monopartite begomoviruses. A GenBank search revealed that the three viruses were previously undescribed. The GZ and SH tomato isolates are herein provisionally named ToLCV-GZ1 (GenBank Accession No. AY044137), ToLCV-GZ2 (GenBank Accession No. AY044138), and ToLCV-SH (GenBank Accession No. AY044139), respectively. All three tomato-infecting begomoviruses have identical stem-loop structures containing the conserved nonanucleotide motif characteristic of all members of the family Geminiviridae; however, the predicted Rep binding element located in the common region is unique for each virus. Phylogenetic analysis of the three viral sequences placed them in a large clade containing all other Old World begomoviruses. Distance comparisons among these and other well-studied begomoviruses indicated that ToLCV-GZ1 and ToLCV-SH shared an overall 90% nucleotide sequence identity, with ˜83% nucleotide sequence identity to ToLCV-GZ2. ToLCV-GZ1 and ToLCV-SH were 83% identical, with their closest relative, Tomato yellow leaf curl virus (TYLCV), while ToLCV-GZ2 shared 93% identity with TYLCV. The genomes of all three Sudan viruses contained regions of homologous nucleotide sequences, suggesting intermolecular exchange among these viruses. Exclusion of the homologous sequences (>800 nt) from the phylogenetic analysis indicated even lower shared nucleotide identities (<90%, the arbitrary cut-off for distinct species), which may warrant their classification as separate species. These three newly described begomoviruses are indigenous to central Sudan, and comprise a unique Old World lineage distinct from previously described begomoviruses associated with leaf curl disease of tomato in Africa and the Mediterranean Region. References: (1) A. M. Idris and J. K. Brown. Phytopathology 83:548, 1998. (2) A. M. Yassin. Trop. Pest Manage. 29:253, 1983.
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DJEKOTA, Christophe, Mame Samba MBAYE, Doudou DIOP, and Kandioura NOBA. "Poils épidermiques, types stomatiques et taxonomie chez les morphotypes de karité Vitellaria paradoxa C.F. Gaertn subsp. paradoxa)." Journal of Animal & Plant Sciences 45, no. 1 (2020): 7758–70. http://dx.doi.org/10.35759/janmplsci.v45-1.1.
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Les poils épidermiques et les types stomatiques chez les morphotypes de karité (Vitellaria paradoxa C.F. Gaertn subsp. paradoxa) ont été étudiés au Tchad en 2010, de Juillet à Septembre. L’objectif est la recherche des caractères micro morphologiques discriminants susceptibles d’améliorer l’identification des morphotypes de cette espèce. En fait, des morphotypes de karité ont été décrits et nommés par les ruraux dans la province du Mandoul au Tchad. Les amandes de karité sont transformées en beurre, ce qui lui confère une importance sur le plan socio-économique. Des fragments de bourgeon apical prélevés sur des jeunes plantes issues de la germination des graines des cinq (5) morphotypes ont permis d’observer les types de poils épidermiques. Aussi, des échantillons de feuilles prélevés distinctement de chaque morphotype ont été préparés selon la méthode de Barfod (1988). Cette méthode a été privilégiée car l’épiderme de la feuille de karité n’est pas facilement détachable. Elle consiste à bouillir les échantillons de feuilles dans de l’eau distillée pendant 10 minutes puis ils sont trempés dans l’acide nitrique à 40% pendant 16 à 20 heures. Cette opération a permis de ramollir le mésophyle et facilite la desquamation de la cuticule. La surface du fragment de la feuille ramollie placée sur une lame de microscope dans une goutte d'eau est grattée délicatement et progressivement à l’aide du bord de ciseaux jusqu'à ce qu'un fragment d'épiderme transparent apparaisse. Les épidermes foliaires ainsi obtenus sont placés dans du Lugol pendant 10 minutes puis montés après rinçage entre lame et lamelle dans la gélatine glycérinée et observés au microscope optique de type MOTIC. Au total 30 dénombrements ont été effectués sur les deux faces soit en moyenne 6 observations par morphotype. Ces dénombrements ont permis de calculer la densité stomatique et l’indice stomatique de chaque morphotype. La densité stomatique est la moyenne des 6 dénombrements par unité de surface (mm²). Les résultats ont montré 4 groupes de morphotypes : 1- des poils épidermiques simples longs observés chez le morphotype A, appelé localement « Bogrombaye » ; 2- des poils simples courts observés Djekota et al., 2020 Journal of Animal & Plant Sciences (J.Anim.Plant Sci. ISSN 2071-7024) Vol.45 (1): 7758-7770 https://doi.org/10.35759/JAnmPlSci.v45-1.1 7759 chez les morphotypes C, E et F « Komane, Mbabète, Ngoïtokoro » ; 3- des poils glanduleux longs observés chez le morphotype D « Meingré » et ; 4- des poils glanduleux courts observés chez le morphotype B « Kiankos ». De plus, des stomates de type anomocytique périgène à subsidiaire dicyclique sont observés chez tous les morphotypes étudiés. La densité stomatique évaluée est 362±5 st/mm² et l’indice stomatique varie de 45,1±0,7% chez les morphotypes de karité étudiés. Ces connaissances pourraient améliorer la systématique des morphotypes et fournir une base pour la sélection du matériel végétal approprié pour les programmes locaux de reboisement et/ou pour la production agronomique, car le beurre de cette espèce est de plus en plus sollicité. Epidermal hair, stomatal types and taxonomy in shea morphotypes (Vitellaria paradoxa C.F. Gaertn subsp. Paradoxa) ABSTRACT Epidermal hair and stomatal types in shea morphotypes (Vitellaria paradoxa C.F. Gaertn subsp. paradoxa) were studied in Chad in 2010, from July to September. The objective is the search for discriminating micro morphological characters likely to improve the identification of the morphotypes of this species. In fact, shea morphotypes have been described and named by rural people in the province of Mandoul in Chad. Shea kernels are transformed into butter, which gives it socio-economic importance. Fragments of the apical bud taken from young plants from the germination of the seeds of the five (5) morphotypes made it possible to observe the types of epidermal hair. Also, leaf samples taken separately from each morphotype were prepared according to the method of Barfod (1988). This method was preferred because the epidermis of the shea leaf is not easily detachable. It involves boiling the leaf samples in distilled water for 10 minutes and then soaking them in 40% nitric acid for 16-20 hours. This operation allowed to soften the mesophyle and facilitates the scaling of the cuticle. The surface of the fragment of the softened leaf placed on a microscope slide in a drop of water is gently and gradually scraped off using the edge of the scissors until a transparent epidermis fragment appears. The leaf epidermis thus obtained are placed in Lugol for 10 minutes and then mounted after rinsing between slide and coverslip in glycerol gelatin and observed under an optical microscope of the MOTIC type. A total of 30 counts were made on both sides, an average of 6 observations per morphotype. These counts made it possible to calculate the stomatal density and the stomatic index of each morphotype. The stomatal density is the average of the 6 counts per unit area (mm²). The results showed 4 groups of morphotypes: 1- long single epidermal hairs observed in morphotype A, locally called "Bogrombaye"; 2- short simple hairs observed in morphotypes C, E and F "Komane, Mbabète, Ngoïtokoro"; 3- long glandular hairs observed in the morphotype D "Meingré" and; 4- short glandular hairs observed in morphotype B "Kiankos". In addition, stomata of the perigenic anomocytic type with dicyclic subsidiary are observed in all the morphotypes studied. The stomatal density evaluated is 362 ± 5 st / mm² and the stomatic index varies from 45.1 ± 0.7% in the shea morphotypes studied. This knowledge could improve the system of morphotypes and provide a basis for the selection of appropriate plant material for local reforestation programs and / or for agronomic production, as butter from this species is in increasing demand.
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Nicolae, Marius, and Sanguthevar Rajasekaran. "qPMS9: An Efficient Algorithm for Quorum Planted Motif Search." Scientific Reports 5, no. 1 (2015). http://dx.doi.org/10.1038/srep07813.
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Abstract Discovering patterns in biological sequences is a crucial problem. For example, the identification of patterns in DNA sequences has resulted in the determination of open reading frames, identification of gene promoter elements, intron/exon splicing sites and SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have led to domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, discovery of short functional motifs, etc. In this paper we focus on the identification of an important class of patterns, namely, motifs. We study the (ℓ, d) motif search problem or Planted Motif Search (PMS). PMS receives as input n strings and two integers ℓ and d. It returns all sequences M of length ℓ that occur in each input string, where each occurrence differs from M in at most d positions. Another formulation is quorum PMS (qPMS), where the motif appears in at least q% of the strings. We introduce qPMS9, a parallel exact qPMS algorithm that offers significant runtime improvements on DNA and protein datasets. qPMS9 solves the challenging DNA (ℓ, d)-instances (28, 12) and (30, 13). The source code is available at https://code.google.com/p/qpms9/.
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"Parallel Algorithms for Discovering Planted (l, d) Motif." International Journal of Innovative Technology and Exploring Engineering 9, no. 4 (2020): 1452–61. http://dx.doi.org/10.35940/ijitee.d1521.029420.
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In computational biology, motifs are short, recurring patterns of biological sequences that possess the principal character for the analysis and interpretation of various biological issues like human disease, gene function, drug design, etc. The major objectives of the motif search problem are the management, analysis, and interpretation of huge biological sequences using computational techniques from computer science and mathematics. However, detection of the motif leads to computational problems whose solutions require a substantial amount of time in one uniprocessor machine and thus, remains as one challenging problem. In this chapter, two parallel algorithms are proposed, along with its implementation detail which crucially enhances the performance of the PMSP motif search algorithm. The first approach enhances the existing algorithm by eliminating the redundant process of the computation and also, minimizes the execution time by the use of both process-level and thread-level parallelism in the implementation. The second approach is the improvement over the first one, where not only the time of computation is reduced further but also the best space utilization is achieved..
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Nicolae, Marius, and Sanguthevar Rajasekaran. "Efficient sequential and parallel algorithms for planted motif search." BMC Bioinformatics 15, no. 1 (2014). http://dx.doi.org/10.1186/1471-2105-15-34.
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Nicolae, Marius, and Sanguthevar Rajasekaran. "Erratum: CORRIGENDUM: qPMS9: An Efficient Algorithm for Quorum Planted Motif Search." Scientific Reports 5, no. 1 (2015). http://dx.doi.org/10.1038/srep09544.
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Yu, Qiang, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, and Jun Huan. "RefSelect: a reference sequence selection algorithm for planted (l, d) motif search." BMC Bioinformatics 17, S9 (2016). http://dx.doi.org/10.1186/s12859-016-1130-6.
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Hasan, Mohammad, Abu Saleh Musa Miah, Md Moazzem Hossain, and Md Sabir Hossain. "LL-PMS8: A time efficient approach to solve planted motif search problem." Journal of King Saud University - Computer and Information Sciences, November 2020. http://dx.doi.org/10.1016/j.jksuci.2020.11.026.
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Yu, Qiang, Yana Hu, Xinnan Hu, Jingfen Lan, and Yang Guo. "An efficient exact algorithm for planted motif search on large DNA sequence datasets." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024, 1–10. http://dx.doi.org/10.1109/tcbb.2024.3404136.
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Hasan, Mohammad, Abu Saleh Musa Miah, Md Humaun Kabir, and Mahmudul Alam. "Trie-PMS8: A Trie-tree based Robust Solution for Planted Motif Search Problem." International Journal of Cognitive Computing in Engineering, July 2024. http://dx.doi.org/10.1016/j.ijcce.2024.07.004.
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Theepalakshmi, P., and U. Srinivasulu Reddy. "Planted (l, d) motif search using Bat algorithm with inertia weight and opposition based learning." International Journal of Information Technology, May 20, 2022. http://dx.doi.org/10.1007/s41870-022-00923-y.
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Yu, Qiang, Dingbang Wei, and Hongwei Huo. "SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets." BMC Bioinformatics 19, no. 1 (2018). http://dx.doi.org/10.1186/s12859-018-2242-y.
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Theepalakshmi, P., та U. Srinivasulu Reddy. "A new efficient quorum planted (ℓ, d) motif search on ChIP-seq dataset using segmentation to filtration and freezing firefly algorithms". Soft Computing, 20 жовтня 2023. http://dx.doi.org/10.1007/s00500-023-09236-z.
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Gunasekara, Chathura, Avinash Subramanian, Janaki Venkata Ram Kumar Avvari, Bin Li, Su Chen, and Hairong Wei. "ExactSearch: a web-based plant motif search tool." Plant Methods 12, no. 1 (2016). http://dx.doi.org/10.1186/s13007-016-0126-6.
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