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Journal articles on the topic 'De novo leaf transcriptome'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Salazar, Juan Alfonso, Cristian Vergara-Pulgar, Claudia Jorquera, et al. "De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources." Agronomy 11, no. 5 (2021): 919. http://dx.doi.org/10.3390/agronomy11050919.

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Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expr

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Kottapalli, Pratibha, Mauricio Ulloa, Kameswara Rao Kottapalli, Paxton Payton, and John Burke. "SNP Marker Discovery in Pima Cotton (Gossypium barbadense L.) Leaf Transcriptomes." Genomics Insights 9 (January 2016): GEI.S40377. http://dx.doi.org/10.4137/gei.s40377.

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The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton ( Gossypium barbadense L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs f

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Sadat-Hosseini, Mohammad, Mohammad Reza Bakhtiarizadeh, Naser Boroomand, Masoud Tohidfar, and Kourosh Vahdati. "Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut." PLOS ONE 15, no. 4 (2020): e0232005. http://dx.doi.org/10.1371/journal.pone.0232005.

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Kaushik, Prashant, and Shashi Kumar. "Data of de novo assembly of the leaf transcriptome in Aegle marmelos." Data in Brief 19 (August 2018): 700–703. http://dx.doi.org/10.1016/j.dib.2018.05.095.

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Eguiluz, M., F. R. Kulcheski, R. Margis, and F. Guzman. "De novo assembly of Vriesea carinata leaf transcriptome to identify candidate cysteine-proteases." Gene 691 (April 2019): 96–105. http://dx.doi.org/10.1016/j.gene.2018.12.053.

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Vitiello, Alessia, Rosa Rao, Giandomenico Corrado, et al. "De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii." Data 3, no. 3 (2018): 36. http://dx.doi.org/10.3390/data3030036.

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Zucchini (Cucurbita pepo L.), extensively cultivated in temperate areas, belongs to the Cucurbitaceae family and it is a species with great economic value. One major threat related to zucchini cultivation is the damage imposed by the cotton/melon aphid Aphis gossypii Glover (Homoptera: Aphididae). We performed RNA-sequencing on cultivar “San Pasquale” leaves, uninfested and infested by A. gossypii, that were collected at three time points (24, 48, and 96 h post infestation). Then, we combined all high-quality reads for de novo assembly of the transcriptome. This resource was primarily establis

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Claude, Sivagami-Jean, Gurusamy Raman, and Seon-Joo Park. "Comparative Analysis and Identification of Terpene Synthase Genes in Convallaria keiskei Leaf, Flower and Root Using RNA-Sequencing Profiling." Plants 12, no. 15 (2023): 2797. http://dx.doi.org/10.3390/plants12152797.

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The ‘Lilly of the Valley’ species, Convallaria, is renowned for its fragrant white flowers and distinctive fresh and green floral scent, attributed to a rich composition of volatile organic compounds (VOCs). However, the molecular mechanisms underlying the biosynthesis of this floral scent remain poorly understood due to a lack of transcriptomic data. In this study, we conducted the first comparative transcriptome analysis of C. keiskei, encompassing the leaf, flower, and root tissues. Our aim was to investigate the terpene synthase (TPS) genes and differential gene expression (DEG) patterns a

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Senn, Savanah, Ray A. Enke, Steven J. Carrell, et al. "De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (Quercus agrifolia)." Applied Microbiology 5, no. 1 (2025): 24. https://doi.org/10.3390/applmicrobiol5010024.

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Coast Live Oak (Quercus agrifolia) is a native keystone hardwood species of the California coastal and semi-arid forest environment. Q. agrifolia is threatened by pathogens such as the oomycete Phytophthora ramorum, which is known to cause Sudden Oak Death in environments from Southern California to Oregon. This study considers oaks and their rootzone microbes recovering from moderate and low-intensity fires in rapid succession, compared to high- and low-intensity fires with a large time gap between them. cDNA libraries from nine oak leaf tissue samples were sequenced on DNBseq. Soil samples w

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Ma, Jikai, Lingmin Wei, Jiayu Li, and Huogen Li. "The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing." Genes 9, no. 12 (2018): 577. http://dx.doi.org/10.3390/genes9120577.

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The leaf, a photosynthetic organ that plays an indispensable role in plant development and growth, has a certain ability to adapt to the environment and exhibits tremendous diversity among angiosperms. Liriodendron chinense, an ancestral angiosperm species, is very popular in landscaping. The leaf of this species has two lobes and resembles a Qing Dynasty Chinese robe; thus, leaf shape is the most valuable ornamental trait of the tree. In this work, to determine the candidate genes associated with leaf development in L. chinense, scanning electron microscopy (SEM) was employed to distinguish t

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Li, Peiling, Maofei Ren, Juanjuan Chen, et al. "Transcriptomic Analysis of Green Leaf Plants and White–Green Leaf Mutants in Haworthia cooperi var. pilifera." Genes 15, no. 5 (2024): 608. http://dx.doi.org/10.3390/genes15050608.

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Haworthia cooperi var. pilifera is a succulent plant with ornamental value. The white–green leaf mutant (wl) showed a significant difference in leaf color from the wild-type plant (WT). In this study, we integrated the transcriptomes of wl and WT plants to screen differentially expressed genes related to leaf color variation. The results of transcriptome analysis showed that 84,163 unigenes were obtained after de novo assembly and the NR database annotated the largest number of unigenes, which accounted for 57.13%, followed by NT (43.02%), GO (39.84%), Swiss-Prot (39.25%), KEGG (36.06%), and C

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Liu, Fu-Mei, Zhou Hong, Zeng-Jiang Yang, Ning-Nan Zhang, Xiao-Jin Liu, and Da-Ping Xu. "De Novo Transcriptome Analysis of Dalbergia odorifera and Transferability of SSR Markers Developed from the Transcriptome." Forests 10, no. 2 (2019): 98. http://dx.doi.org/10.3390/f10020098.

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Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads w

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Kang, Yang Jae, Jayern Lee, Yong Hwan Kim, and Suk-Ha Lee. "Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis." Plant Genetic Resources 12, S1 (2014): S21—S26. http://dx.doi.org/10.1017/s1479262114000185.

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Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a ref

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Shi, Yuanyuan, Shengxiang Zhang, Daiyin Peng, et al. "De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis." PeerJ 8 (November 6, 2020): e10157. http://dx.doi.org/10.7717/peerj.10157.

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Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of th

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Lyu, Y. Z., X. Y. Dong, L. B. Huang, and L. S. Huang. "De novo assembly of Koelreuteria transcriptome and analysis of major gene related to leaf etiolation." South African Journal of Botany 113 (November 2017): 355–61. http://dx.doi.org/10.1016/j.sajb.2017.09.004.

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Foong, Lian Chee, Anthony Siong Hock Ho, Brandon Pei Hui Yeo, Yang Mooi Lim, and Sheh May Tam. "Data of de novo assembly and functional annotation of the leaf transcriptome of Impatiens balsamina." Data in Brief 23 (April 2019): 103603. http://dx.doi.org/10.1016/j.dib.2018.12.042.

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Tomescu, Mihai-Silviu, Selisha Ann Sooklal, Thuto Ntsowe, et al. "Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)." PLOS ONE 16, no. 7 (2021): e0253741. http://dx.doi.org/10.1371/journal.pone.0253741.

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The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transc

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Wimberley, James, Joseph Cahill, and Hagop S. Atamian. "De novo Sequencing and Analysis of Salvia hispanica Tissue-Specific Transcriptome and Identification of Genes Involved in Terpenoid Biosynthesis." Plants 9, no. 3 (2020): 405. http://dx.doi.org/10.3390/plants9030405.

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Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which repre

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Miryeganeh, Matin, and Hidetoshi Saze. "De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)." International Journal of Molecular Sciences 22, no. 18 (2021): 9874. http://dx.doi.org/10.3390/ijms22189874.

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Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and

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Frias-Soler, Roberto Carlos, Lilian Villarín Pildaín, Agnes Hotz-Wagenblatt, Jonas Kolibius, Franz Bairlein, and Michael Wink. "De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe)." PeerJ 6 (November 20, 2018): e5860. http://dx.doi.org/10.7717/peerj.5860.

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We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almo

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Liu, Shichao, Siming Wang, Meichen Liu, et al. "De novo sequencing and analysis of the transcriptome of Panax ginseng in the leaf-expansion period." Molecular Medicine Reports 14, no. 2 (2016): 1404–12. http://dx.doi.org/10.3892/mmr.2016.5376.

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Adil, L., and Purushothaman Natarajan. "De novo assembly and analysis of Solanum trilobatum L. leaf transcriptome using next generation sequencing technology." Canadian Journal of Biotechnology 1, Special Issue (2017): 186. http://dx.doi.org/10.24870/cjb.2017-a172.

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22

Meera, S. P., Anusha Sreeshan, and Anu Augustine. "Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam." Data in Brief 31 (August 2020): 105747. http://dx.doi.org/10.1016/j.dib.2020.105747.

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23

Rai, Amit, Taiki Nakaya, Yohei Shimizu, et al. "De Novo Transcriptome Assembly and Characterization of Lithospermum officinale to Discover Putative Genes Involved in Specialized Metabolites Biosynthesis." Planta Medica 84, no. 12/13 (2018): 920–34. http://dx.doi.org/10.1055/a-0630-5925.

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Abstract Lithospermum officinale is a valuable source of bioactive metabolites with medicinal and industrial values. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. This study presents the first effort to establish and characterize de novo transcriptome assembly resource for L. officinale and expression analysis for three of its tissues, namely leaf, stem, and root. Using over 4Gbps of RNA-sequencing datasets, we obtained de novo transcriptome assembly of L. officinale, consisting of 77,047

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Wei, Fu-Jin, Saneyoshi Ueno, Tokuko Ujino-Ihara, et al. "Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1)." PLOS ONE 16, no. 2 (2021): e0247180. http://dx.doi.org/10.1371/journal.pone.0247180.

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Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated prot

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Wang, Yalin, Wenyan Zhu, Fei Ren, Na Zhao, Shixiao Xu, and Ping Sun. "Transcriptional Memory in Taraxacum mongolicum in Response to Long-Term Different Grazing Intensities." Plants 11, no. 17 (2022): 2251. http://dx.doi.org/10.3390/plants11172251.

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Grazing, as an important land use method in grassland, has a significant impact on the morphological and physiological traits of plants. However, little is known about how the molecular mechanism of plant responds to different grazing intensities. Here, we investigated the response of Taraxacum mongolicum to light grazing and heavy grazing intensities in comparison with a non-grazing control. Using de novo transcriptome assembly, T. mongolicum leaves were compared for the expression of the different genes under different grazing intensities in natural grassland. In total, 194,253 transcripts w

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Kumar Kushwaha, Sandeep, Ramesh R. Vetukuri, Firuz Odilbekov, Nidhi Pareek, Tina Henriksson, and Aakash Chawade. "Differential Gene Expression Analysis of Wheat Breeding Lines Reveal Molecular Insights in Yellow Rust Resistance under Field Conditions." Agronomy 10, no. 12 (2020): 1888. http://dx.doi.org/10.3390/agronomy10121888.

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The evolution of pathogens in the changing climate raises new challenges for wheat production. Yellow rust is one of the major wheat diseases worldwide, leading to an increased use of fungicides to prevent significant yield losses. The enhancement of the resistance potential of wheat cultivars is a necessary and environmentally friendly solution for sustainable wheat production. In this study, we aimed to identify the differentially expressed genes induced upon yellow rust infection in the field. Reference and de novo based transcriptome analysis was performed among the resistant and susceptib

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Yang, Shiwen, Kehao Liang, Aibin Wang, Ming Zhang, Jiangming Qiu, and Lingyun Zhang. "Physiological Characterization and Transcriptome Analysis of Camellia oleifera Abel. during Leaf Senescence." Forests 11, no. 8 (2020): 812. http://dx.doi.org/10.3390/f11080812.

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Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so leaf senescence, the final stage of leaf development, is an important agronomic trait affecting the production and quality of tea oil. However, the physiological characteristics and molecular mechanism underlying leaf senescence of C. oleifera are poorly understood. In this study, we performed physiological observation and de novo transcripto

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Sicilia, Angelo, Gorgio Testa, Danilo Fabrizio Santoro, Salvatore Luciano Cosentino, Angela Roberta, and Lo Piero. "RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under longterm salt stress." BMC Plant Biology 2019 (June 4, 2019): 19:335. https://doi.org/10.1186/s12870-019-1964-y.

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To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 extreme).The picture that emerges from the identification of differentially expressed genes is consistent with a salt dose-dependent response. Hence, a deeper re programming of the gene expression occurs in those plants grew at extreme salt level than in those subjected to severe salt stress, probably representing for the

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Prasidhee, V., and Purushothaman Natarajan. "Sequencing, De novo Assembly, Functional Annotation and Analysis of Cardiospermum halicacabum L. Leaf Transcriptome Using Illumina Platform." Canadian Journal of Biotechnology 1, Special Issue (2017): 190. http://dx.doi.org/10.24870/cjb.2017-a176.

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Evangelistella, Chiara, Alessio Valentini, Riccardo Ludovisi, et al. "De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock." Biotechnology for Biofuels 10, no. 1 (2017): 138. https://doi.org/10.1186/s13068-017-0828-7.

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<strong>Background: </strong> <i>Arundo donax</i> has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.<strong>Results: </strong>We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the <i>A. donax</i> leaf transcriptome. The s

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Upadhyay, Swati, Ujjal J. Phukan, Sonal Mishra, and Rakesh Shukla. "De novo leaf and root transcriptome analysis identified novel genes involved in Steroidal sapogenin biosynthesis in Asparagus racemosus." BMC Genomics 15, no. 1 (2014): 746. http://dx.doi.org/10.1186/1471-2164-15-746.

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Bains, Savita, Vasundhara Thakur, Jagdeep Kaur, Kashmir Singh, and Ravneet Kaur. "Elucidating genes involved in sesquiterpenoid and flavonoid biosynthetic pathways in Saussurea lappa by de novo leaf transcriptome analysis." Genomics 111, no. 6 (2019): 1474–82. http://dx.doi.org/10.1016/j.ygeno.2018.09.022.

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Yang, Yan Hui, Ming Jie Li, Xin Jian Chen, et al. "De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease." Molecular Breeding 34, no. 3 (2014): 905–15. http://dx.doi.org/10.1007/s11032-014-0084-5.

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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (December 28, 2017): 16. http://dx.doi.org/10.12688/gatesopenres.12783.1.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised the si

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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (February 13, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.2.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a sing

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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition." Gates Open Research 1 (March 8, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.3.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a sing

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Zhang, Yanzhao, Shuzhen Xu, Yanwei Cheng, Zhengfeng Peng, and Jianming Han. "Transcriptome profiling of anthocyanin-related genes reveals effects of light intensity on anthocyanin biosynthesis in red leaf lettuce." PeerJ 6 (April 13, 2018): e4607. http://dx.doi.org/10.7717/peerj.4607.

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Red leaf lettuce (Lactuca sativaL.) is popular due to its high anthocyanin content, but poor leaf coloring often occurs under low light intensity. In order to reveal the mechanisms of anthocyanins affected by light intensity, we compared the transcriptome ofL. sativaL. var.capitataunder light intensities of 40 and 100 μmol m−2s−1. A total of 62,111 unigenes were de novo assembled with an N50 of 1,681 bp, and 48,435 unigenes were functionally annotated in public databases. A total of 3,899 differentially expressed genes (DEGs) were detected, of which 1,377 unigenes were up-regulated and 2,552 u

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de Souza, V. C., M. M. Aragão, L. S. Tavares, P. V. S. Z. Capriles, L. F. Viccini, and M. O. Santos. "De novo leaf transcriptome of a triploid linalool chemotype of Lippia alba (Mill.) N.E.Br. ex Britton & P. Wilson." Brazilian Journal of Botany 44, no. 4 (2021): 889–901. http://dx.doi.org/10.1007/s40415-021-00771-3.

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Gao, Meiling, Siyu Yao, Yang Liu, et al. "Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors." International Journal of Molecular Sciences 19, no. 1 (2017): 31. http://dx.doi.org/10.3390/ijms19010031.

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Alsamadany, Hameed. "De novo leaf transcriptome assembly of Bougainvillea spectabilis for the identification of genes involves in the secondary metabolite pathways." Gene 746 (July 2020): 144660. http://dx.doi.org/10.1016/j.gene.2020.144660.

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Wu, Hualing, Dong Chen, Jiaxian Li, et al. "De Novo Characterization of Leaf Transcriptome Using 454 Sequencing and Development of EST-SSR Markers in Tea (Camellia sinensis)." Plant Molecular Biology Reporter 31, no. 3 (2012): 524–38. http://dx.doi.org/10.1007/s11105-012-0519-2.

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Wang, Gang, Xilong Du, Jing Ji, Chunfeng Guan, Zhaodi Li, and Tchouopou Lontchi Josine. "De novo characterization of the Lycium chinense Mill. leaf transcriptome and analysis of candidate genes involved in carotenoid biosynthesis." Gene 555, no. 2 (2015): 458–63. http://dx.doi.org/10.1016/j.gene.2014.10.058.

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Buitimea-Cantúa, Génesis V., and Jorge Molina-Torres. "De novo transcriptome sequencing, assembly and characterization of Heliopsis longipes roots vs. leaves to discover putative genes involved in specialized metabolites biosynthesis." Plant Omics, no. 14(01):2021 (September 10, 2021): 11–22. http://dx.doi.org/10.21475/poj.14.01.21.p3067.

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Heliopsis longipes is a valuable source of specialized metabolites (or secondary metabolites) with medicinal properties mainly in roots. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. In this work, the genes of the biosynthetic pathway of the specialized metabolism from H. longipes roots and leaves through de novo RNA sequencing (RNA-Seq) using the platform of Illumina paired-end sequencing were studied. After de novo transcriptome assembly using the software Newbler, a total of 172,342 non

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Sun, Huapeng, Fang Li, Zijian Xu, et al. "De novo leaf and root transcriptome analysis to identify putative genes involved in triterpenoid saponins biosynthesis in Hedera helix L." PLOS ONE 12, no. 8 (2017): e0182243. http://dx.doi.org/10.1371/journal.pone.0182243.

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Shi, Yun-Long, Yue-Yue Sheng, Zhuo-Yu Cai, et al. "Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling." International Journal of Molecular Sciences 20, no. 10 (2019): 2439. http://dx.doi.org/10.3390/ijms20102439.

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Anthracnose is a major leaf disease in tea plant induced by Colletotrichum, which has led to substantial losses in yield and quality of tea. The molecular mechanism with regards to responses or resistance to anthracnose in tea remains unclear. A de novo transcriptome assembly dataset was generated from healthy and anthracnose-infected leaves on tea cultivars “Longjing-43” (LJ43) and “Zhenong-139” (ZN139), with 381.52 million pair-end reads, encompassing 47.78 billion bases. The unigenes were annotated versus Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), National Center fo

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ZHAO, Shuang, and Chenshu WANG. "Deep sequencing and transcriptome analyses to identify genes involved in iridoid biosynthesis in the medicinal plant Valeriana jatamansi Jones." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 48, no. 1 (2020): 189–99. http://dx.doi.org/10.15835/nbha48111759.

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Valeriana jatamansi Jones is utilized for medicinal purposes in China, and is also an important substitute for European Valeriana officinalis. The major active principles are generally called valepotriates, which belong to iridoids compounds. To better understand the iridoid biosynthesis pathway in V. jatamansi, we generated transcriptome sequences from the leaf and root tissues, and performed de novo sequence assembly, a total of 183,524,060 transcripts and 61,876 unigenes for V. jatamansi were obtained from 13.28 Gb clean reads. 56,641 unigenes were annotated by public databases, while 5,235

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Zheng, Jie, Xiangjun Kong, Bin Li, et al. "Comparative Transcriptome Analysis between a Novel Allohexaploid Cotton Progeny CMS Line LD6A and Its Maintainer Line LD6B." International Journal of Molecular Sciences 20, no. 24 (2019): 6127. http://dx.doi.org/10.3390/ijms20246127.

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Cytoplasmic male sterility (CMS) is an important agronomic feature and provides an effective tool for heterosis utilization of crops. This study reports the comparative transcriptomic sketches between a novel allohexaploid cotton progeny CMS line LD6A and its maintainer line LD6B using de novo transcriptome sequencing technology at the pollen abortion stage. A total of 128,901 Unigenes were identified, in which 2007 were upregulated and 11,864 were downregulated. The significantly differentially expressed genes (DEGs) in LD6A show a distant and diverse genetic nature due to their distant hybri

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Zhang, Ting, Miaomiao Wang, Zhaoju Li, Xien Wu, and Xiaoli Liu. "Transcriptome analysis and exploration of genes involved in the biosynthesis of secoiridoids in Gentiana rhodantha." PeerJ 11 (March 8, 2023): e14968. http://dx.doi.org/10.7717/peerj.14968.

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Gentiana rhodantha is a medicinally important perennial herb used as traditional Chinese and ethnic medicines. Secoiridoids are one of the major bioactive compounds in G. rhodantha. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from four organs (root, leaf, stem and flower), followed by the de novo sequence assembly. We verified 8-HGO (8-hydroxygeraniol oxidoreductase), which may encode key enzymes of the secoiridoid biosynthesis by qRT-PCR. The mangiferin, swertiamarin and loganic acid contents in root, stem, leaf, and flower were determined b

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Wang, Ying, Kun Liu, De Bi, Shoubiao Zhou, and Jianwen Shao. "Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China." PeerJ 5 (June 15, 2017): e3422. http://dx.doi.org/10.7717/peerj.3422.

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Background Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence

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Rai, Manoj K., Jatan K. Shekhawat, Vinod Kataria, and N. S. Shekhawat. "De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria , a multipurpose tree of Indian Thar Desert." Plant Gene 12 (December 2017): 88–97. http://dx.doi.org/10.1016/j.plgene.2017.09.002.

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