Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

Publication Overview
TitleTranscriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery
AuthorsKaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW
TypeJournal Article
Journal NameBMC genomics
Volume12
Year2011
Page(s)265
CitationKaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC genomics. 2011; 12:265.

Abstract

BACKGROUND
Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality.

RESULTS
Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs). De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR)-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism.

CONCLUSIONS
A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

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Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Language Abbreng
Journal CountryEngland
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2011
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-12-265
Elocation10.1186/1471-2164-12-265
LanguageEnglish
Publication TypeResearch Support, Non-U.S. Gov't