Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

Publication Overview
TitleComprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
AuthorsFranssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber AP
TypeJournal Article
Journal NameBMC genomics
Volume12
Year2011
Page(s)227
CitationFranssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber AP. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC genomics. 2011; 12:227.

Abstract

BACKGROUND
The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic resources exist.

RESULTS
We analyzed the pea transcriptome at the highest possible amount of accuracy by current technology. We used next generation sequencing with the Roche/454 platform and evaluated and compared a variety of approaches, including diverse tissue libraries, normalization, alternative sequencing technologies, saturation estimation and diverse assembly strategies. We generated libraries from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings, comprising a total of 450 megabases. Libraries were assembled into 324,428 unigenes in a first pass assembly.A second pass assembly reduced the amount to 81,449 unigenes but caused a significant number of chimeras. Analyses of the assemblies identified the assembly step as a major possibility for improvement. By recording frequencies of Arabidopsis orthologs hit by randomly drawn reads and fitting parameters of the saturation curve we concluded that sequencing was exhaustive. For leaf libraries we found normalization allows partial recovery of expression strength aside the desired effect of increased coverage. Based on theoretical and biological considerations we concluded that the sequence reads in the database tagged the vast majority of transcripts in the aerial tissues. A pathway representation analysis showed the merits of sampling multiple aerial tissues to increase the number of tagged genes. All results have been made available as a fully annotated database in fasta format.

CONCLUSIONS
We conclude that the approach taken resulted in a high quality - dataset which serves well as a first comprehensive reference set for the model legume pea. We suggest future deep sequencing transcriptome projects of species lacking a genomics backbone will need to concentrate mainly on resolving the issues of redundancy and paralogy during transcriptome assembly.

Features
This publication contains information about 84,267 features:
Feature NameUniquenameType
JI961398JI961398.1region
JI961397JI961397.1region
JI961396JI961396.1region
JI961395JI961395.1region
JI961394JI961394.1region
JI961393JI961393.1region
JI961392JI961392.1region
JI961391JI961391.1region
JI961390JI961390.1region
JI961389JI961389.1region
JI961388JI961388.1region
JI961387JI961387.1region
JI961386JI961386.1region
JI961385JI961385.1region
JI961384JI961384.1region
JI961383JI961383.1region
JI961382JI961382.1region
JI961381JI961381.1region
JI961380JI961380.1region
JI961379JI961379.1region
JI961378JI961378.1region
JI961377JI961377.1region
JI961376JI961376.1region
JI961375JI961375.1region
JI961374JI961374.1region

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication Date2011
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-12-227
Elocation10.1186/1471-2164-12-227
Journal CountryEngland
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Publication TypeResearch Support, Non-U.S. Gov't