Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome

Publication Overview
TitleDevelopment of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome
AuthorsVerma P, Shah N, Bhatia S
TypeJournal Article
Journal NamePlant biotechnology journal
Volume11
Issue7
Year2013
Page(s)894-905
CitationVerma P, Shah N, Bhatia S. Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome. Plant biotechnology journal. 2013 Sep; 11(7):894-905.

Abstract

Genomic resources such as ESTs, molecular markers and linkage maps are essential for crop improvement. However, these resources are still limited in important legumes such as lentil (Lens culinaris Medik.), which is valued world wide as a rich source of dietary protein. In this study, the de novo transcriptome assembly of 119,855,798 short reads, generated by Illumina paired-end sequencing, was performed using various assembly programs. This resulted in 42,196 nonredundant high-quality transcripts of average length 810 bases, N50 value of 1,432 and an average expression per transcript of 26.21 rpkm reads per kilobase per million(RPKM). Similarity search with the unigenes and protein sequences of other plants resulted in maximum similarity with soybean. A total of 20,009 nonredundant transcripts showed similarity with the UniProtKB database and of these, 18,064 transcripts were grouped into three main GO categories, that is, biological process (15,126), molecular function (15,505) and cellular component (9,434). Annotated transcripts were mapped to 289 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 8,893 transcripts were classified into 24 functional categories based on Cluster of Orthologous Groups (COG) of proteins. Mining the data set for the presence of SSRs resulted in 8,722 SSRs with a frequency occurrence of one SSR per 3.92 kb. From these, 5,673 SSR primer pairs were designed, and a subset of these were utilized for diversity analysis. This study, which provides a large data set of annotated transcripts and gene-based SSR markers, would serve as a foundation for various applications in lentil breeding and genetics.

Features
This publication contains information about 54 features:
Feature NameUniquenameType
LcESSR1LcESSR1genetic_marker
LcESSR11LcESSR11genetic_marker
LcESSR12LcESSR12genetic_marker
LcESSR13LcESSR13genetic_marker
LcESSR15LcESSR15genetic_marker
LcESSR16LcESSR16genetic_marker
LcESSR18LcESSR18genetic_marker
LcESSR19LcESSR19genetic_marker
LcESSR2LcESSR2genetic_marker
LcESSR21LcESSR21genetic_marker
LcESSR23LcESSR23genetic_marker
LcESSR24LcESSR24genetic_marker
LcESSR25LcESSR25genetic_marker
LcESSR26LcESSR26genetic_marker
LcESSR28LcESSR28genetic_marker
LcESSR30LcESSR30genetic_marker
LcESSR33LcESSR33genetic_marker
LcESSR34LcESSR34genetic_marker
LcESSR35LcESSR35genetic_marker
LcESSR36LcESSR36genetic_marker
LcESSR39LcESSR39genetic_marker
LcESSR43LcESSR43genetic_marker
LcESSR44LcESSR44genetic_marker
LcESSR47LcESSR47genetic_marker
LcESSR48LcESSR48genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Journal CountryEngland
DOI10.1111/pbi.12082
Elocation10.1111/pbi.12082
Publication ModelPrint-Electronic
ISSN1467-7652
eISSN1467-7652
Publication Date2013 Sep
Journal AbbreviationPlant Biotechnol. J.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Copyright© 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
Publication TypeResearch Support, Non-U.S. Gov't
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:23759076