XTBG OpenIR  > 生态进化组
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species
Brousseau, L; Tinaut, A; Duret, C; Lang, TG; Garnier-Gere, P; Scotti, I
2014
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume15Issue:xPages:238
AbstractBackground: The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. Results: In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over-or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/ 100 bp in variation-containing contigs. Conclusion: The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
Keyword454-pyrosequencing Tropical Rainforest Tree Species Polymorphism Discovery
Language英语
Document Type期刊论文
Identifierhttp://ir.xtbg.org.cn/handle/353005/5080
Collection生态进化组
Recommended Citation
GB/T 7714
Brousseau, L,Tinaut, A,Duret, C,et al. High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species[J]. BMC GENOMICS,2014,15(x):238.
APA Brousseau, L,Tinaut, A,Duret, C,Lang, TG,Garnier-Gere, P,&Scotti, I.(2014).High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.BMC GENOMICS,15(x),238.
MLA Brousseau, L,et al."High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species".BMC GENOMICS 15.x(2014):238.
Files in This Item: Download All
File Name/Size DocType Version Access License
High-throughput tran(1116KB) 开放获取CC BY-NC-SAView Download
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Brousseau, L]'s Articles
[Tinaut, A]'s Articles
[Duret, C]'s Articles
Baidu academic
Similar articles in Baidu academic
[Brousseau, L]'s Articles
[Tinaut, A]'s Articles
[Duret, C]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Brousseau, L]'s Articles
[Tinaut, A]'s Articles
[Duret, C]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.pdf
Format: Adobe PDF
This file does not support browsing at this time
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.