A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus Cajan L.) Using Sanger and Second-generation Sequencing Platforms

Overview

Journal Mol Plant

Publisher Cell Press

Specialties Biology
Molecular Biology

Date 2012 Jan 14

PMID 22241453

Citations 33

Authors

Himabindu Kudapa

Arvind K Bharti

Steven B Cannon

Andrew D Farmer

Benjamin Mulaosmanovic

Robin Kramer

Abhishek Bohra

Nathan T Weeks

John A Crow

Reetu Tuteja

Trushar Shah

Sutapa Dutta

Deepak K Gupta

Archana Singh

Kishor Gaikwad

Tilak R Sharma

Gregory D May

Nagendra K Singh

Rajeev K Varshney

Affiliations

Soon will be listed here.

Abstract

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ~8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs). By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping positions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content (PIC) value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

Citing Articles

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