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
JI925072JI925072.1region
JI925071JI925071.1region
JI925070JI925070.1region
JI925069JI925069.1region
JI925068JI925068.1region
JI925067JI925067.1region
JI925066JI925066.1region
JI925065JI925065.1region
JI925064JI925064.1region
JI925063JI925063.1region
JI925062JI925062.1region
JI925061JI925061.1region
JI925060JI925060.1region
JI925059JI925059.1region
JI925058JI925058.1region
JI925057JI925057.1region
JI925056JI925056.1region
JI925055JI925055.1region
JI925054JI925054.1region
JI925053JI925053.1region
JI925052JI925052.1region
JI925051JI925051.1region
JI925050JI925050.1region
JI925049JI925049.1region
JI925048JI925048.1region

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