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Journal articles on the topic 'Genome collinearity'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Stirling, Brigid, Zamin Koo Yang, Lee E. Gunter, Gerald A. Tuskan, and H. D. Bradshaw Jr. "Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity." Canadian Journal of Forest Research 33, no. 11 (2003): 2245–51. http://dx.doi.org/10.1139/x03-155.

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More than 300 kb of DNA sequence from five Populus bacterial artificial chromosome (BAC) clones was compared with the complete sequence of the Arabidopsis genome to search for collinearity between the genomes of these two plant genera. Approximately 27% of the DNA sequences from the Populus genome were homologous to protein-coding regions in the Arabidopsis genome. BLAST scores and synteny were used to infer orthologous relationships between the Populus and Arabidopsis homologs. The probability that any pair of genes on a single Populus BAC will have orthologs on the same Arabidopsis chromosom

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Xu, Yiqing, Changwei Bi, Guoxin Wu, et al. "VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/7823429.

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Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, t

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Liu, Longxiang, Shuai Peng, Weiyu Song, Hongyu Zhao, Hua Li, and Hua Wang. "Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a." Polish Journal of Microbiology 71, no. 2 (2022): 279–92. http://dx.doi.org/10.33073/pjm-2022-026.

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Abstract Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic

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Yang, Jia, Jinxuan Wen, Simin Xiao, et al. "Complete Genome and Molecular Characterization of a New Cyprinid Herpesvirus 2 (CyHV-2) SH-01 Strain Isolated from Cultured Crucian Carp." Viruses 14, no. 9 (2022): 2068. http://dx.doi.org/10.3390/v14092068.

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Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during outbreaks in crucian carp at a local fish farm near Shanghai, China. CyHV-2 SH-01 exhibited a high sensitivity to goldfish and crucian carp in our previous research. The complete genome of SH-01 is 290,428 bp with 154 potential open reading frames (ORFs) and terminal repeat (TR) regions at both ends. Compared to the se

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Parkin, I. AP, D. J. Lydiate, and M. Trick. "Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5." Genome 45, no. 2 (2002): 356–66. http://dx.doi.org/10.1139/g01-160.

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This study describes a comprehensive comparison of chromosome 5 of the model crucifer Arabidopsis with the genome of its amphidiploid crop relative Brassica napus and introduces the use of in silico sequence homology to identify conserved loci between the two species. A region of chromosome 5, spanning 8 Mb, was found in six highly conserved copies in the B. napus genome. A single inversion appeared to be the predominant rearrangement that had separated the two lineages leading to the formation of Arabidopsis chromosome 5 and its homologues in B. napus. The observed results could be explained

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Kong, Lingyang, Lengleng Ma, Shan Jiang, et al. "Genome-Wide Identification, Exogenous Hormone Response, Gene Structure, and Conserved Motif Analysis of the GRF Gene Family in Cerasus humilis." Biology 14, no. 7 (2025): 763. https://doi.org/10.3390/biology14070763.

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The Cerasus humilis, a perennial shrub belonging to the Cerasus genus, is native to China and holds significant ecological and economic importance. Growth regulation factors (GRF) are a family of transcription factors (TF) that play a key role in plant growth and development. This research entailed an in-depth examination of the GRF family in C. humilis, exploring its significance in the evolution of C. humilis. Twelve GRF genes were identified in the C. humilis genome. Named separately as ChGRF1-Chumilis15987.1, ChGRF2-Chumilis25207.1, ChGRF3-Chumilis26233.1, ChGRF4-Chumilis08578.3, ChGRF5-Ch

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Gaiero, Paola, José van de Belt, Francisco Vilaró, M. Eric Schranz, Pablo Speranza, and Hans de Jong. "Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping." Genome 60, no. 3 (2017): 228–40. http://dx.doi.org/10.1139/gen-2016-0150.

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A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their corr

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Udall, Joshua A., Evan Long, Chris Hanson, et al. "De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri." G3: Genes|Genomes|Genetics 9, no. 10 (2019): 3079–85. http://dx.doi.org/10.1534/g3.119.400392.

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Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sa

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Heraghty, Sam D., John M. Sutton, Meaghan L. Pimsler, Janna L. Fierst, James P. Strange, and Jeffrey D. Lozier. "De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii." G3: Genes|Genomes|Genetics 10, no. 8 (2020): 2585–92. http://dx.doi.org/10.1534/g3.120.401437.

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Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annot

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Xu, Yiqing, Qi'ang Wang, Luis Tanon Reyes, et al. "VGSC2: Second generation vector graph toolkit of genome synteny and collinearity." Genomics 112, no. 1 (2020): 286–88. http://dx.doi.org/10.1016/j.ygeno.2019.02.007.

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Bennetzin, Jeffrey L., and Michael Freeling. "Grasses as a single genetic system: genome composition, collinearity and compatibility." Trends in Genetics 9, no. 8 (1993): 259–61. http://dx.doi.org/10.1016/0168-9525(93)90001-x.

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Ying, Jianchao, Jun Ye, Teng Xu, Qian Wang, Qiyu Bao, and Aifang Li. "Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution." International Journal of Genomics 2019 (December 20, 2019): 1–14. http://dx.doi.org/10.1155/2019/8987436.

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Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages.

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Li, Shoujian, Bing Li, and Shunxing Guo. "Chromosome-Level Assembly Reveals a Fifteen-Chromosome Aneuploid Genome and Environmental Adaptation Strategy of Chinese Traditional Medical Fungus Wolfiporia hoelen." International Journal of Molecular Sciences 25, no. 16 (2024): 8786. http://dx.doi.org/10.3390/ijms25168786.

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The sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and foods commonly used in China, Japan, Korea, and other Asian countries. To provide a high-quality reference genome and deepen our understanding of the genome of W. hoelen to elucidate various biological phenomena. In this study, we assembled three genomes of W. hoelen using a combination of Nanopore and Illumina sequencing strategies. The fifteen-chromosome genome L7 of W. hoelen was assembled with two-sided telomere and rDNA sequences for the first time. The chromosome count was subsequently conf

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Li, Tang, Jinfang Zheng, Orestis Nousias, et al. "The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis." Plants 13, no. 5 (2024): 636. http://dx.doi.org/10.3390/plants13050636.

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Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya ‘Booth’ cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity an

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Zeng, Zhefei, Chunmin Mao, Zhuo Shang, et al. "Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Hippophae salicifolia." Biology 14, no. 4 (2025): 448. https://doi.org/10.3390/biology14040448.

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This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 tRNA, three rRNA, and three pseudogenes). We identified extensive repetitive elements, including 188 SSRs, 20 tandem repeats, and 455 dispersed repeats, and explored their potential roles in genome evolution. Codon usage analysis showed a bias for codons ending in A or U, while RNA editing analysis revealed 415 sites

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Moskal, Kinga, Sylwia Kowalik, Wiesław Podyma, Bogusław Łapiński, and Maja Boczkowska. "The Pros and Cons of Rye Chromatin Introgression into Wheat Genome." Agronomy 11, no. 3 (2021): 456. http://dx.doi.org/10.3390/agronomy11030456.

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Rye is one of the most commonly used sources of elite genes in wheat improvement programs. Due to the high collinearity of the genomes of both cereal species, it is possible to obtain interspecific chromosomal translocations and substitution lines. Rye chromatin is used to transfer numerous genes for resistance to biotic and abiotic stresses into the wheat genome. Introgression has also resulted in improved agronomic traits. However, despite the numerous advantages, the transfer of large fragments or whole chromosomes has been quite often accompanied by a decrease in end-use quality. This pape

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Xu, Su, Jianjun Cheng, Xiangchen Meng, Yan Xu, and Ying Mu. "Complete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces." Evolutionary Bioinformatics 16 (January 2020): 117693432094219. http://dx.doi.org/10.1177/1176934320942192.

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Lactobacillus reuteri YSJL-12 was isolated from healthy sow fresh feces and used as probiotics additives previously. To investigate the genetic basis on probiotic potential and identify the genes in the strain, the complete genome of YSJL-12 was sequenced. Then comparative genome analysis on 9 strains of Lactobacillus reuteri was performed. The genome of YSJL-12 consisted of a circular 2,084,748 bp chromosome and 2 circular plasmids (51,906 and 15,134 bp). From among the 2065 protein-coding sequences (CDSs), the genes resistant to the environmental stress were identified. The function of COG (

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Papageorgiou, Spyros. "Physical Laws Shape Up HOX Gene Collinearity." Journal of Developmental Biology 9, no. 2 (2021): 17. http://dx.doi.org/10.3390/jdb9020017.

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Hox gene collinearity (HGC) is a multi-scalar property of many animal phyla particularly important in embryogenesis. It relates entities and events occurring in Hox clusters inside the chromosome DNA and in embryonic tissues. These two entities differ in linear size by more than four orders of magnitude. HGC is observed as spatial collinearity (SC), where the Hox genes are located in the order (Hox1, Hox2, Hox3 …) along the 3′ to 5′ direction of DNA in the genome and a corresponding sequence of ontogenetic units (E1, E2, E3, …) located along the Anterior—Posterior axis of the embryo. Expressio

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Jakubowska, Agata K., Sander A. Peters, Jadwiga Ziemnicka, Just M. Vlak, and Monique M. van Oers. "Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exigua multiple NPV." Journal of General Virology 87, no. 3 (2006): 537–51. http://dx.doi.org/10.1099/vir.0.81461-0.

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The genome sequence of a Polish isolate of Agrotis segetum nucleopolyhedrovirus (AgseNPV-A) was determined and analysed. The circular genome is composed of 147 544 bp and has a G+C content of 45·7 mol%. It contains 153 putative, non-overlapping open reading frames (ORFs) encoding predicted proteins of more than 50 aa, together making up 89·8 % of the genome. The remaining 10·2 % of the DNA constitutes non-coding regions and homologous-repeat regions. One hundred and forty-three AgseNPV-A ORFs are homologues of previously reported baculovirus gene sequences. There are ten unique ORFs and they a

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Wang, Xi, Yu Xiao, Zi-Han He, Ling-Ling Li, Yan-Wen Lv, and Xin-Sheng Hu. "Evolutionary Divergence between Toona ciliata and Toona sinensis Assayed with Their Whole Genome Sequences." Genes 13, no. 10 (2022): 1799. http://dx.doi.org/10.3390/genes13101799.

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Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was cultivated as an economic and nutritious tree for more than 2000 years. The two species differ in flower and leaf morphological traits, reproductive systems, and range size of natural distribution. To reveal the potential molecular basis of these divergences, we examined the similarities and differences in their whole genome sequences. Results indic

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Cheng, Hua, Xiaohua Huang, Shuai Wu, et al. "Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi." Biomolecules 12, no. 12 (2022): 1731. http://dx.doi.org/10.3390/biom12121731.

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Pueraria lobata (wild.) Ohwi is a leguminous plant and one of the traditional Chinese herbal medicines. Its puerarin extract is widely used in the pharmaceutical industry. This study reported a chromosome-level genome assembly for P. lobata and its characteristics. The genome size was ~939.2 Mb, with a contig N50 of 29.51 Mbp. Approximately 97.82% of the assembled sequences were represented by 11 pseudochromosomes. We identified that the repetitive sequences accounted for 63.50% of the P. lobata genome. A total of 33,171 coding genes were predicted, of which 97.34% could predict the function.

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Xu, Xiao, Xinyu Wang, Sirui Zhou, et al. "Genome-Wide Identification and Characterization of the OFP Gene Family in the Wild Strawberry Fragaria vesca." Agronomy 14, no. 3 (2024): 569. http://dx.doi.org/10.3390/agronomy14030569.

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OVATE family proteins (OFPs) are a kind of plant-specific transcription factor, which play important roles in the growth and development of plants. Here, we performed a genome-wide investigation of the OFP gene family members in the wild diploid strawberry (Fragaria vesca, 2n = 14), and analyzed their physical and chemical properties, gene structure, phylogeny, expression patterns, and the subcellular localizations of these genes. Fourteen OFP genes from F.vesca were identified. Collinearity analysis showed ten pairs of collinearity between F. vesca and Arabidopsis. Phylogenetic analysis divid

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Zhang, Jinzhu, Yu Mo, Shuai Chen, et al. "Identification of Dof Transcription Factors in the Genome of Rosa chinensis." Journal of the American Society for Horticultural Science 147, no. 5 (2022): 239–48. http://dx.doi.org/10.21273/jashs05150-21.

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The DNA binding with one finger (Dof), as an important transcription factor, plays an important role in growth and development, primary and secondary metabolism, stress resistance, and plant hormone signal transduction. However, the identification and analysis of the Dof transcription factor family in Rosa is rarely reported. In this study, 28 Rosa chinensis Dof (RcDof) members were identified, which were located on seven chromosomes. The RcDofs were divided into 12 subfamilies according to evolutionary analysis. Through motif, gene structure, and cis-acting element analyses of the 12 subfamil

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Papageorgiou, Spyros. "Disappearance of Temporal Collinearity in Vertebrates and Its Eventual Reappearance." Biology 10, no. 10 (2021): 1018. http://dx.doi.org/10.3390/biology10101018.

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It was observed that a cluster of ordered genes (Hox1, Hox2, Hox3…) in the genome are activated in the ontogenetic units (1, 2, 3 …) of an embryo along the Anterior/Posterior axis following the same order of the Hox genes. This Spatial Collinearity (SC) is very strange since it correlates events of very different spatial dimensions. It was later observed in vertebrates, that, in the above ordering, first is Hox1expressed in ontogenetic unit 1, followed later by Hox2 in unit 2 and even later Hox3 in unit 3. This temporal collinearity (TC) is an enigma and even to-day is explored in depth. In 19

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Yang, Yanmei, Jinpeng Wang, and Jianyong Di. "Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome." International Journal of Genomics 2013 (2013): 1–4. http://dx.doi.org/10.1155/2013/275616.

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Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication accoun

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Li, Xiaomei, Le Liang, Jianzhao Ran, et al. "Re-Sequencing the Mitochondrial Genome Unveils a Novel Isomeric Form of NWB CMS Line in Radish and Functional Verification of Its Candidate Sterile Gene." Horticulturae 10, no. 4 (2024): 395. http://dx.doi.org/10.3390/horticulturae10040395.

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Radish (Raphanus sativus L.) is a globally significant vegetable and relies on cytoplasmic male sterile (CMS) lines for hybrid seed production. The NWB CMS type is favored over Ogura CMS for its ease in maintainer screening. Despite its varied mitochondrial configurations and unvalidated sterile gene, we re-sequenced the mitochondrial genome of NWB CMS Tibet A and verified the function of the sterility gene via genetic transformation of Arabidopsis thaliana. The mitochondrial genomes of Tibet A could be assembled into circular DNA molecules, with a mitochondrial genome size of 239,184 bp. Our

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Yang, Hongyu, Wenxia Yao, Xiangjun Fan, Yang Lu, Yan Wang, and Zonghuan Ma. "Genome-Wide Identification and Analysis of WD40 Family and Its Expression in F. vesca at Different Coloring Stages." International Journal of Molecular Sciences 25, no. 22 (2024): 12334. http://dx.doi.org/10.3390/ijms252212334.

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WD40 proteins play important roles in the synthesis and regulation of anthocyanin, the regulation of plant morphology and development, and the response to various abiotic stresses. However, the role of WD40 in Fragaria vesca (F. vesca) has not been studied. In this study, a total of 216 FvWD40 family members were identified, which were divided into four subfamilies based on evolutionary tree analysis. Subcellular localization predictions show that FvWD40 family members are mainly localized in chloroplasts, nuclei, and cytoplasm. An analysis of collinearity revealed a total of eight pairs of in

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Tao, Xiaoyan, Bo Liu, and Quanwen Dou. "The Kengyilia hirsuta karyotype polymorphisms as revealed by FISH with tandem repeats and single-gene probes." Comparative Cytogenetics 15, no. 4 (2021): 375–92. http://dx.doi.org/10.3897/compcytogen.v15.i4.71525.

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Kengyilia hirsuta (Keng, 1959) J. L. Yang, C. Yen et B. R. Baum, 1992, a perennial hexaploidy species, is a wild relative species to wheat with great potential for wheat improvement and domestication. The genome structure and cross-species homoeology of K. hirsuta chromosomes with wheat were assayed using 14 single-gene probes covering all seven homoeologous groups, and four repetitive sequence probes 45S rDNA, 5S rDNA, pAs1, and (AAG)10 by FISH. Each chromosome of K. hirsuta was well characterized by homoeological determination and repeats distribution patterns. The synteny of chromosomes was

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Tao, Xiaoyan, Bo Liu, and Quanwen Dou. "The Kengyilia hirsuta karyotype polymorphisms as revealed by FISH with tandem repeats and single-gene probes." Comparative Cytogenetics 15, no. (4) (2021): 375–92. https://doi.org/10.3897/compcytogen.v15.i4.71525.

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Kengyilia hirsuta (Keng, 1959) J. L. Yang, C. Yen et B. R. Baum, 1992, a perennial hexaploidy species, is a wild relative species to wheat with great potential for wheat improvement and domestication. The genome structure and cross-species homoeology of K. hirsuta chromosomes with wheat were assayed using 14 single-gene probes covering all seven homoeologous groups, and four repetitive sequence probes 45S rDNA, 5S rDNA, pAs1, and (AAG)<sub>10</sub> by FISH. Each chromosome of K. hirsuta was well characterized by homoeological determination and repeats distribution patterns. The synteny of chro

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Hu, Xin, Yingquan Zhang, Jingjuan Zhang, et al. "Consensus Genetic Linkage Map Construction Based on One Common Parental Line for QTL Mapping in Wheat." Agronomy 11, no. 2 (2021): 227. http://dx.doi.org/10.3390/agronomy11020227.

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The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSe

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Papageorgiou, Spyros. "Hox Gene Collinearity with Pulling Physical Forces Creates a Hox Gene Clustering in Embryos of Vertebrates and Invertebrates: Complete or Split Clusters." Symmetry 16, no. 5 (2024): 594. http://dx.doi.org/10.3390/sym16050594.

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Hox gene clusters are crucial in embryogenesis. It was observed that some Hox genes are located in order along the telomeric to centromeric direction of the DNA sequence: Hox1, Hox2, Hox3…. These genes are expressed in the same order in the ontogenetic units of the Drosophila embryo along the anterior–posterior axis. The two entities (genome and embryo) differ significantly in linear size and in-between distance. This strange phenomenon was named spatial collinearity (SP). Later, it was observed that, particularly in the vertebrates, a temporal collinearity (TC) coexists: first Hox1 is express

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Ramli, Siti Roszilawati, Boyke Bunk, Cathrin Spröer, et al. "Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes." Pathogens 10, no. 9 (2021): 1198. http://dx.doi.org/10.3390/pathogens10091198.

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The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical L. interrogans isolates from Malaysia. All six contained the larger (4.28–4.56 Mb) and smaller (0.34–0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0–7 p

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Liu, Xiqiang, Han Zhang, Lin Ma, Zan Wang, and Kun Wang. "Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family Under Abiotic Stresses in Medicago truncatula." Genes 11, no. 11 (2020): 1389. http://dx.doi.org/10.3390/genes11111389.

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The trihelix transcription factor (GT) family is widely involved in regulating plant growth and development, and most importantly, responding to various abiotic stresses. Our study first reported the genome-wide identification and analysis of GT family genes in Medicago truncatula. Overall, 38 trihelix genes were identified in the M. truncatula genome and were classified into five subfamilies (GT-1, GT-2, SH4, GTγ and SIP1). We systematically analyzed the phylogenetic relationship, chromosomal distribution, tandem and segmental duplication events, gene structures and conserved motifs of MtGTs.

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An, Mengya, Ruoxi Liang, Yanliu Chen, et al. "Chromosome-Level Genome Assembly and Annotation of the Highly Heterozygous Phallus echinovolvatus Provide New Insights into Its Genetics." Journal of Fungi 11, no. 1 (2025): 62. https://doi.org/10.3390/jof11010062.

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Phallus echinovolvatus is a well-known edible and medicinal fungus with significant economic value. However, the available whole-genome information is lacking for this species. The chromosome-scale reference genome (Monop) and two haploid genomes (Hap1 and Hap2) of P. echinovolvatus, each assembled into 11 pseudochromosomes, were constructed using Illumina, PacBio-HiFi long-read sequencing, and Hi-C technology. The Monop had a size of 36.54 Mb, with 10,251 predicted protein-coding genes and including 433 carbohydrate-active enzyme genes, 385 cytochrome P450 enzyme genes, and 42 gene clusters r

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Pan, Weiqiang, Mincong Liang, Yanlin You, et al. "Viral genomic methylation and the interspecies evolutionary relationships of ranavirus." PLOS Pathogens 20, no. 11 (2024): e1012736. http://dx.doi.org/10.1371/journal.ppat.1012736.

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Ranaviruses are capable of infecting both wild and farmed fish, amphibians, and reptiles, leading to significant economic losses and ecological risks. Currently, ranaviruses have been found in at least 175 species spanning six continents. Except for Singapore grouper iridovirus (SGIV), ranavirus genomes are generally regarded as highly methylated. Nevertheless, our comprehension of the methylation characteristics within ranaviruses remains limited. Despite the numerous genomes currently included in the GenBank database, a complete phylogenetic tree for ranaviruses has not yet been determined,

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Xu, Yiqing, Changwei Bi, Guoxin Wu, et al. "Corrigendum to “VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity”." BioMed Research International 2016 (2016): 1. http://dx.doi.org/10.1155/2016/4948583.

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Ji, Gaoxiang, Ying Long, Guangqin Cai, et al. "Whole-Genome Comparison Reveals Structural Variations behind Heading Leaf Trait in Brassica oleracea." International Journal of Molecular Sciences 24, no. 4 (2023): 4063. http://dx.doi.org/10.3390/ijms24044063.

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Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome tripl

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Hao, Lidong, Jinshan Zhang, Shubing Shi, et al. "Identification and expression profiles of the YABBY transcription factors in wheat." PeerJ 10 (February 3, 2022): e12855. http://dx.doi.org/10.7717/peerj.12855.

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Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship

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Wei, Hui, Ali Movahedi, Guoyuan Liu, et al. "Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Gene Family and Its Expression in Response to Abiotic Stress in Poplar." International Journal of Molecular Sciences 23, no. 3 (2022): 1418. http://dx.doi.org/10.3390/ijms23031418.

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Carotenoid cleavage dioxygenases (CCDs) catalyzes the cleavage of various carotenoids into smaller apocarotenoids which are essential for plant growth and development and response to abiotic stresses. CCD family is divided into two subfamilies: 9-cis epoxycarotenoid dioxygenases (NCED) family and CCD family. A better knowledge of carotenoid biosynthesis and degradation could be useful for regulating carotenoid contents. Here, 23 CCD genes were identified from the Populus trichocarpa genome, and their characterizations and expression profiling were validated. The PtCCD members were divided into

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Yu, Liyiqi, Jichun Xia, Rujiao Jiang, et al. "Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed (Brassica napus L.)." International Journal of Molecular Sciences 25, no. 10 (2024): 5301. http://dx.doi.org/10.3390/ijms25105301.

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The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, an

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Li, Ruimiao, Cuiyun Lei, Qiang Zhang, et al. "Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet." Plants 14, no. 8 (2025): 1257. https://doi.org/10.3390/plants14081257.

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The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (xm and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (Accession_SiSRSN[.n]_xDy or xTy) was proposed to unify gene family nomenclature, enabling the direct visualiza

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Cavell, A. C., D. J. Lydiate, IAP Parkin, C. Dean, and M. Trick. "Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome." Genome 41, no. 1 (1998): 62–69. http://dx.doi.org/10.1139/g97-097.

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Arabidopsis thaliana (the model dicotyledonous plant) is closely related to Brassica crop species. Genome collinearity, or conservation of marker order, between Brassica napus (oilseed rape) and A. thaliana was assessed over a 7.5-Mbp region of the long arm of A. thaliana chromosome 4, equivalent to 30 cM. Estimates of copy number indicated that sequences present in a single copy in the haploid genome of A. thaliana (n = 5) were present in 2-8 copies in the haploid genome of B. napus (n = 19), while sequences present in multiple copies in A. thaliana were present in over 10 copies in B. napus.

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Xia, Dongnan, Lulu Guan, Yue Yin, et al. "Genome-Wide Analysis of MBF1 Family Genes in Five Solanaceous Plants and Functional Analysis of SlER24 in Salt Stress." International Journal of Molecular Sciences 24, no. 18 (2023): 13965. http://dx.doi.org/10.3390/ijms241813965.

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Multiprotein bridging factor 1 (MBF1) is an ancient family of transcription coactivators that play a crucial role in the response of plants to abiotic stress. In this study, we analyzed the genomic data of five Solanaceae plants and identified a total of 21 MBF1 genes. The expansion of MBF1a and MBF1b subfamilies was attributed to whole-genome duplication (WGD), and the expansion of the MBF1c subfamily occurred through transposed duplication (TRD). Collinearity analysis within Solanaceae species revealed collinearity between members of the MBF1a and MBF1b subfamilies, whereas the MBF1c subfami

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He, Lei, Chen Lu, Xi Yan, et al. "Genome-Wide Identification of the Polygalacturonase Gene Family and Its Potential Association with Abscission Zone in Capsicum annuum L." Genes 16, no. 5 (2025): 579. https://doi.org/10.3390/genes16050579.

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Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized by structural, evolutionary, and comparative genomic analyses. Their expression profiles across various tissues and fruit development stages were examined using transcriptome data. Ethephon treatment and qRT-PCR were employed to assess gene responses during ethylene-induced pedicel absciss

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Wang, Hui, Qianhua Tang, Jinyan Mao, et al. "Genome-Wide Comparative Analysis of Invertases in the Salicaceae with the Identification of Genes Involved in Catkin Fiber Initiation and Development." Current Issues in Molecular Biology 47, no. 6 (2025): 423. https://doi.org/10.3390/cimb47060423.

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Invertase (INV) irreversibly converts sucrose to glucose and fructose during processes such as differentiation and organ development in plants, especially during the development of trichomes. Systematic identification and analysis of INVs in Salicaceae remain limited. Here, INV genes in Populus deltoides and Salix suchowensis were investigated, and their chromosomal localization, collinearity, gene structures, cis-regulatory elements, and phylogenetic relationships were comprehensively analyzed. Twenty and seventeen INVs were found, respectively, in P. deltoides and S. suchowensis, most of whi

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Xu, Yiqing, Changwei Bi, Guoxin Wu, et al. "Corrigendum #2 to “VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity”." BioMed Research International 2019 (May 30, 2019): 1. http://dx.doi.org/10.1155/2019/2150291.

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Zhang, Shengcheng, Hejun Du, Xingtan Zhang, and Binzhong Wang. "CATG: Software for Collinearity-Based Genome Assembly Correction." G3: Genes, Genomes, Genetics, November 22, 2024. http://dx.doi.org/10.1093/g3journal/jkae277.

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Abstract Genome assembly errors can have a profound effect on downstream analyses. Collinearity-based Assembly Correction Tool (CATG) is designed to rectify these errors by leveraging collinearity information between the assembled genome and a reference genome. CATG provides a user-friendly interface for visualizing and manually correcting assembly errors. It supports various operations such as insertion, deletion, inversion, and swapping of contigs and chromosomes. The software automatically re-clusters, re-labels, and re-draws the assembly after each modification, ensuring that users can eas

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YANG, Qiuhong, Dongyun ZUO, Hailiang CHENG, et al. "Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly." Journal of Cotton Research 4, no. 1 (2021). http://dx.doi.org/10.1186/s42397-021-00096-2.

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Abstract Introduction Genome sequence plays an important role in both basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of upland cotton (G. hirsutum), highlights the need to improve the genome quality rapidly and efficiently. Methods We performed Hi-C sequencing of G. raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We also compared the reassembled genome sequence with the previously published G. raimondii genomes for gene and genome sequence collinearity. Result A total of 98.42% of scaffold seq

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Lampar, Adam, András Farkas, László Ivanizs, et al. "A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat." Plant Genome 18, no. 1 (2025). https://doi.org/10.1002/tpg2.70009.

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AbstractGoatgrasses with U‐ and M‐genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F2 individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromos

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Li, Cheng, David Wickell, Li-Yaung Kuo, et al. "Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes." Proceedings of the National Academy of Sciences 121, no. 4 (2024). http://dx.doi.org/10.1073/pnas.2312607121.

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Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes ( Selaginella and Isoetes ) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum . Remarkably, despite that the two species diverged ~350 Mya, around 30% o

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