Journal Article

FZJ-2017-06698

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png De novo Transcriptome Analysis of Miscanthus Iutarioriparius Indentifies Candidate Genes in Rhizome Development

Hu, R. ; Yu, C. ; Wang, X. ; Jia, C.-L.FZJ* ; Pei, S. ; He, K. ; He, G. ; Kong, Y. ; Zhou, G. (Corresponding author)

2017
Frontiers Media Lausanne

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Please use a persistent id in citations: http://hdl.handle.net/2128/15324  doi:10.3389/fpls.2017.00492

Abstract: Miscanthus 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.

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Contributing Institute(s):

1. Physik Nanoskaliger Systeme (ER-C-1)

Research Program(s):

1. 143 - Controlling Configuration-Based Phenomena (POF3-143) (POF3-143)

Appears in the scientific report 2017

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Database coverage:
; ; ; ; BIOSIS Previews ; Current Contents - Agriculture, Biology and Environmental Sciences ; DOAJ Seal ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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