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De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development
Hu, Ruibo1; Yu, Changjiang1; Wang, Xiaoyu1; Jia, Chunlin2; Pei, Shengqiang1; He, Kang1; He, Guo1; Kong, Yingzhen3; Zhou, Gongke1
2017-04-12
Source PublicationFRONTIERS IN PLANT SCIENCE
Volume8
AbstractMiscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M. lutarioriparius with an emphasis to identify putative genes involved in rhizome development. Approximately 66 gigabase (GB) paired-end clean reads were obtained and assembled into 169,064 unigenes with an average length of 759 bp. Among these unigenes, 103,899 (61.5%) were annotated in seven public protein databases. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218, and 1,077 genes were predominantly expressed in root, leaf, stem, lateral bud, and rhizome bud, respectively. Their expression patterns were further classified into 12 distinct clusters. Pathway enrichment analysis revealed that genes predominantly expressed in rhizome bud were mainly involved in primary metabolism and hormone signaling and transduction pathways. Noteworthy, 19 transcription factors (TFs) and 16 hormone signaling pathway-related genes were identified to be predominantly expressed in rhizome bud compared with the other tissues, suggesting putative roles in rhizome formation and development. In addition, a predictive regulatory network was constructed between four TFs and six auxin and abscisic acid (ABA) -related genes. Furthermore, the expression of 24 rhizome-specific genes was further validated by quantitative real-time RT-PCR (qRT-PCR) analysis. Taken together, this study provide a global portrait of gene expression across five different tissues and reveal preliminary insights into rhizome growth and development. The data presented will contribute to our understanding of the molecular mechanisms underlying rhizome development in M. lutarioriparius and remarkably enrich the genomic resources of Miscanthus.
SubtypeArticle
KeywordMiscanthus Lutarioriparius Rhizome Formation Rna-seq Lateral Meristem Transcription Factor
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
DOI10.3389/fpls.2017.00492
WOS KeywordDIFFERENTIAL EXPRESSION ANALYSIS ; ORYZA-LONGISTAMINATA ; ENERGY CROPS ; MOLECULAR ANALYSIS ; REVEALS ; GROWTH ; RICE ; DOMESTICATION ; SPECIFICITY ; MORPHOLOGY
Indexed BySCI
Language英语
WOS Research AreaPlant Sciences
Funding OrganizationNational Key Technology Support Program of China(2013BAD22B01) ; Joint Funds of the National Natural Science Foundation of China(U1432126) ; Science and Technology Major Project of Shandong(2015ZDJS03001) ; Youth Innovation Promotion Association of CAS(2014187) ; Taishan Scholar Program of Shandong ; Youth Talent Plan of Chinese Academy of Agricultural Sciences
WOS SubjectPlant Sciences
WOS IDWOS:000398993000001
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qibebt.ac.cn/handle/337004/9286
Collection资源植物与环境工程研究组
Affiliation1.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao Engn Res Ctr Biomass Resources & Environm, Key Lab Biofuels, Qingdao, Peoples R China
2.Shandong Inst Agr Sustainable Dev, Jinan, Peoples R China
3.Chinese Acad Agr Sci, Tobacco Res Inst, Key Lab Tobacco Genet Improvement & Biotechnol, Qingdao, Peoples R China
Recommended Citation
GB/T 7714
Hu, Ruibo,Yu, Changjiang,Wang, Xiaoyu,et al. De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development[J]. FRONTIERS IN PLANT SCIENCE,2017,8.
APA Hu, Ruibo.,Yu, Changjiang.,Wang, Xiaoyu.,Jia, Chunlin.,Pei, Shengqiang.,...&Zhou, Gongke.(2017).De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development.FRONTIERS IN PLANT SCIENCE,8.
MLA Hu, Ruibo,et al."De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development".FRONTIERS IN PLANT SCIENCE 8(2017).
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