De Novo Assembly and Discovery of Genes That Involved in Drought Tolerance in the Common Vetch

Zhu, Yongqun; Liu, Qiuxu; Xu, Weifeng; Zhang, Jianhua; Xie, Wenjie; Nie, Gang; Yao, Li; Wang, Hong; Lin, Chao-Wen

doi:10.3390/ijms20020328

Cited by 23 publications

(21 citation statements)

References 60 publications

(57 reference statements)

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“…High-quality transcripts were obtained from common vetch by PacBio Iso-Seq Single-molecule sequencing offers longer read lengths and higher consensus accuracies, which enable the generation of full-length transcripts and near referencequality genome assemblies, and the accuracy of genome annotation and transcriptome characterization are greatly enhanced, especially for species without reference genomes [23,24]. In the present study, a total of 30,427 full-length transcripts were generated; which is much longer than the previously reported common vetch transcriptome data, such as 772 bp [25], 1124 bp [30] and 921.55 bp [34]. Of these full-length transcripts had a higher annotated percentage than that recognized in previous studies of common vetch (66.10 and 83.48%) [25,30].…”

Section: Discussionmentioning

confidence: 84%

“…In the present study, a total of 30,427 full-length transcripts were generated; which is much longer than the previously reported common vetch transcriptome data, such as 772 bp [25], 1124 bp [30] and 921.55 bp [34]. Of these full-length transcripts had a higher annotated percentage than that recognized in previous studies of common vetch (66.10 and 83.48%) [25,30]. The remaining unannotated transcripts (528) may represent a common vetch-specific and novel gene pool, which will provide a good starting point in future experiments, including the preliminary functional characterization and investigation of their potential roles in drought stress responses in common vetch.…”

Section: Discussionmentioning

confidence: 91%

“…Therefore, systematically recognising the molecular mechanisms of the response to drought is essential for the improvement of the quality and ecological distribution of common vetch. Previously, Zhu et al (2019) performed a de novo transcriptional analysis of whole common vetch plants under drought stress and revealed that drought-responsive genes are mainly involved in plant hormone signal transduction, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis [30]. However, given that most of the sequencing results from NGS cannot represent fulllength cDNA sequences, and the authors only focused on how whole common vetch plants response to drought stress, additional efforts are needed to elucidate and compare the molecular mechanisms systematically between above-and underground tissues of common vetch during the response to drought with full-length sequencing approach.…”

Section: Introductionmentioning

confidence: 99%

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Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

et al. 2020

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Background: Common vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress. Results: Our results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ 1 -pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses. Conclusion:The multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.

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Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

et al. 2020

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“…Therefore, a large number of unigenes have not been annotated, and only 61.7% of the total unigenes were annotated in at least one database. This is different to the annotation results of transcriptome sequencing of reported species, such as common vetch, which has approximately 500 million clean reads employed to assemble 174,636 transcripts and 83.48% unigenes annotated in at least one database [ 28 ]. In the common buckwheat, 53,404 unigenes were assembled, and 39.33% unigenes were annotated in the GO database [ 29 ], whereas 8426 and 12,642 unigenes of Taxus species were annotated in the KEGG and GO database, respectively [ 30 ].…”

Section: Discussionmentioning

confidence: 91%

Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

et al. 2021

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Background Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass. Results A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions. Conclusions Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.

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“…Although the conditions in which these treatments have been performed are not comparable to those presented in our work, some genes and activated routes are similar to those identified in our studies. In both analyses there is a transcriptional enrichment of relevant GO Biological Process categories as "oxidoreductase activity", "redox process", "metabolic process" "cell wall modification" or "carbohydrate metabolic process" [33].…”

Section: Discussionmentioning

confidence: 99%

Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools

2020

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Background: Common vetch (Vicia sativa L.) is a forage grain legume of high protein content and high nitrogen fixation, relevant in sustainable agriculture systems. Drought is the main limiting factor of this crop yield. Genetic resources collections are essential to provide genetic variability for breeding. The analysis of drought associated parameters has allowed us to identify drought tolerant and sensitive ecotypes in a vetch core collection. Results: To understand the mechanisms involved in drought response we analysed transcriptomic differences between tolerant and sensitive accessions. Polymorphic variants (SNPs and SSRs) in these differential expressed genes (DEGs) have also been analysed for the design of drought-associated markers. A total of 1332 transcripts were commonly deregulated in both genotypes under drought. To know the drought adaptive response, we also analysed DEGs between accessions. A total of 2646 transcripts are DEG between sensitive and tolerant ecotypes, in watered and drought conditions, including important genes involved in redox homeostasis, cell wall modifications and stress-response. The integration of this functional and genetic information will contribute to understand the molecular mechanisms of drought response and the adaptive mechanisms of drought tolerance in common vetch. The identification of polymorphic variants in these DEGs has also been screened for the design of droughtassociated markers that could be used in future breeding program strategies. Conclusions: Our studies shed light for the first time in common vetch about the genes and pathways associated with drought tolerance. In addition, we identify over 100 potential drought associated polymorphism, as SNPs or SSRs, which are differently present in drought and tolerant genotypes. The use of these molecular markers for trait prediction would enable the development of genomic tools for future engineering strategies by screening of germplasm crop collections for traits related with crop drought resilience, adaptability or yield in vetch.

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De Novo Assembly and Discovery of Genes That Involved in Drought Tolerance in the Common Vetch

Cited by 23 publications

References 60 publications

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools

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