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
JI965773JI965773.1region
JI965772JI965772.1region
JI965771JI965771.1region
JI965770JI965770.1region
JI965769JI965769.1region
JI965768JI965768.1region
JI965767JI965767.1region
JI965766JI965766.1region
JI965765JI965765.1region
JI965764JI965764.1region
JI965763JI965763.1region
JI965762JI965762.1region
JI965761JI965761.1region
JI965760JI965760.1region
JI965759JI965759.1region
JI965758JI965758.1region
JI965757JI965757.1region
JI965756JI965756.1region
JI965755JI965755.1region
JI965754JI965754.1region
JI965753JI965753.1region
JI965752JI965752.1region
JI965751JI965751.1region
JI965750JI965750.1region
JI965749JI965749.1region

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