De novo assembly and characterisation of the field pea transcriptome using RNA-Seq

Publication Overview
TitleDe novo assembly and characterisation of the field pea transcriptome using RNA-Seq
AuthorsSudheesh S, Sawbridge TI, Cogan NO, Kennedy P, Forster JW, Kaur S
TypeJournal Article
Journal NameBMC genomics
Volume16
Issue1
Year2015
Page(s)611
CitationSudheesh S, Sawbridge TI, Cogan NO, Kennedy P, Forster JW, Kaur S. De novo assembly and characterisation of the field pea transcriptome using RNA-Seq. BMC genomics. 2015; 16(1):611.

Abstract

BACKGROUND
Field pea (Pisum sativum L.) is a cool-season grain legume that is cultivated world-wide for both human consumption and stock-feed purposes. Enhancement of genetic and genomic resources for field pea will permit improved understanding of the control of traits relevant to crop productivity and quality. Advances in second-generation sequencing and associated bioinformatics analysis now provide unprecedented opportunities for the development of such resources. The objective of this study was to perform transcriptome sequencing and characterisation from two genotypes of field pea that differ in terms of seed and plant morphological characteristics.

RESULTS
Transcriptome sequencing was performed with RNA templates from multiple tissues of the field pea genotypes Kaspa and Parafield. Tissue samples were collected at various growth stages, and a total of 23 cDNA libraries were sequenced using Illumina high-throughput sequencing platforms. A total of 407 and 352 million paired-end reads from the Kaspa and Parafield transcriptomes, respectively were assembled into 129,282 and 149,272 contigs, which were filtered on the basis of known gene annotations, presence of open reading frames (ORFs), reciprocal matches and degree of coverage. Totals of 126,335 contigs from Kaspa and 145,730 from Parafield were subsequently selected as the reference set. Reciprocal sequence analysis revealed that c. 87 % of contigs were expressed in both cultivars, while a small proportion were unique to each genotype. Reads from different libraries were aligned to the genotype-specific assemblies in order to identify and characterise expression of contigs on a tissue-specific basis, of which 87 % were expressed in more than one tissue, while others showed distinct expression patterns in specific tissues, providing unique transcriptome signatures.

CONCLUSION
This study provided a comprehensive assembled and annotated transcriptome set for field pea that can be used for development of genetic markers, in order to assess genetic diversity, construct linkage maps, perform trait-dissection and implement whole-genome selection strategies in varietal improvement programs, as well to identify target genes for genetic modification approaches on the basis of annotation and expression analysis. In addition, the reference field pea transcriptome will prove highly valuable for comparative genomics studies and construction of a finalised genome sequence.

Features
This publication contains information about 271,056 features:
Feature NameUniquenameType
GCMO01019501GCMO01019501.1region
GCMO01019502GCMO01019502.1region
GCMO01019503GCMO01019503.1region
GCMO01019504GCMO01019504.1region
GCMO01019505GCMO01019505.1region
GCMO01019506GCMO01019506.1region
GCMO01019507GCMO01019507.1region
GCMO01019508GCMO01019508.1region
GCMO01019509GCMO01019509.1region
GCMO01019510GCMO01019510.1region
GCMO01019511GCMO01019511.1region
GCMO01019512GCMO01019512.1region
GCMO01019513GCMO01019513.1region
GCMO01019514GCMO01019514.1region
GCMO01019515GCMO01019515.1region
GCMO01019516GCMO01019516.1region
GCMO01019517GCMO01019517.1region
GCMO01019518GCMO01019518.1region
GCMO01019519GCMO01019519.1region
GCMO01019520GCMO01019520.1region
GCMO01019521GCMO01019521.1region
GCMO01019522GCMO01019522.1region
GCMO01019523GCMO01019523.1region
GCMO01019524GCMO01019524.1region
GCMO01019525GCMO01019525.1region

Pages

Properties
Additional details for this publication include:
Property NameValue
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2015
Journal AbbreviationBMC Genomics
DOI10.1186/s12864-015-1815-7
Elocation10.1186/s12864-015-1815-7