Transcriptome profiling of Populus tomentosa under cold stress

Yang, Xiaoyu; Zhao, Tianyun; Rao, Pian; Gao, Kai; Yang, Xiong; Chen, Zhong; An, Xinmin

doi:10.1016/j.indcrop.2019.04.056

Cited by 67 publications

(44 citation statements)

References 89 publications

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“…These annotated sequences lay a foundation for further studies of genetic differentiation in P. wulianensis. It has been previously reported that P. tomentosa best matches P. trichocarpa in the NR database 41 , and the species-based annotation performed in the present study also showed that P. wulianensis was most closely related to P. trichocarpa. However, in contrast to P. trichocarpa (sect.…”

Section: Discussionsupporting

confidence: 80%

“…Transcriptome research is one of the essential tools for understanding the life processes of species 38 . Based on next-generation sequencing (NGS), researchers have performed a large number of gene expression and quantitative studies of Populus species [39][40][41] . Zhang et al characterized cDNA libraries of mature xylem from tension wood (72.17%), opposite wood (70.13%), and normal wood (73.58%) of P. tomentosa, and their results showed that the length of most of the transcripts (more than 70%) was approximately 500-1000 bp 42 .…”

Section: Discussionmentioning

confidence: 99%

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Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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“…12 TFs differentially expressed in both genotypes under NaCl treatment were indenti ed in the transcriptome analysis, including three MYBs (AUR62042086, AUR62034188 and AUR62030018), four NACs (AUR62000536, AUR62029344, AUR62015630 and AUR62006885), three WRKYs (AUR62030836, AUR62026996 and AUR62006427), and two ZFPs (AUR62042998 and AUR62009622). It has been shown that two ZFP members Zat10 and Zat12 could be induced by salinity stress in Arabidopsis [70,71], while the two homologous genes in quinoa were highly up-regulated as well in this study, which indicated their potential roles in salt stress. Apart from four WRKYs and four MYBs, one ERF (AUR62028234) and one bZIP (AUR62010368) were also found in the DEGs exclusively in ST genotype, all of which were strongly induced in response to salt stress, suggesting their probable functions in improved salt tolerance.…”

Section: Transcription Factors Related To Salt Stress In Quinoasupporting

confidence: 53%

Transcriptome Analysis and Differential Gene Expression Profiling of Two Contrasting Quinoa Genotypes in Response to Salt Stress

Shi¹,

Gu²

2020

Preprint

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Background: Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.Results: The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. 117 DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions: We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

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“…RNA sequencing (RNA-seq) enables the study of gene expression at the transcriptome level and identifies genes involved in plant-specific biological processes [33][34][35]. So far, with the introduction of a new generation of RNAseq, transcriptome sequencing technology has been used for identify low temperature stress response genes in Ipomoea batatas [36], Brassica napus [37], Populus tomentosa [38], Capsicum annuum [39], and Magnolia wufengensis [40]. In addition, studies on differentially expressed genes of low temperature resistance of alfalfa varieties have also been reported.…”

Section: Introductionmentioning

confidence: 99%

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

Wang

Jin

Meng

et al. 2019

Preprint

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Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown of alfalfa is an important storage organ in the process of wintering, and it is closely related to the winter hardiness of alfalfa. At present, the specific molecular mechanism of response to winter hardiness in alfalfa root crown is unclear. The transcriptome database created by RNA sequencing (RNA-seq) is widely used to identify the critical genes related to winter hardiness. Results: The transcriptomes of alfalfa varieties, such as “Lomgmu 806” (with high winter survival rate) and “Sardi” (with low winter survival rate) have been sequenced in the study. Among the identified 57,712 unigenes, 2,299 differentially expressed genes (DEGs) were up-regulated, and 2,143 unigenes were down-regulated in the Lomgmu 806 vs Sardi root crown. The KEGG pathway annotations showed that 1,159 unigenes were mainly annotated to 116 pathways. Seven DEGs belonging to “plant hormone signaling transduction”, “peroxidase” pathway and transcription factors family (MYB, B3, AP2/ERF, WRKY) genes involved in alfalfa winter hardiness. Among them, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliable results of transcriptome sequencing analyses. Conclusions: RNA-Seq was used to discover genes associated with the wintering differences between alfalfa varieties. The transcriptome data showed that the gene regulation response of alfalfa to low temperature stress, which provides a valuable resource for further identification and functional analysis of candidate genes for winter hardiness of alfalfa. In addition, these data provide references for future study of genetic breeding and winter hardiness in alfalfa.

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Transcriptome profiling of Populus tomentosa under cold stress

Cited by 67 publications

References 89 publications

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Transcriptome Analysis and Differential Gene Expression Profiling of Two Contrasting Quinoa Genotypes in Response to Salt Stress

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

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