A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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...

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Published in分子植物：英文版 Vol. 5; no. 5; pp. 1020 - 1028
Main Author Himabindu Kudapa Arvind K. Bharti Steven B. Cannon Andrew D. Farmer Benjamin Mulaosmanovi 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
Format Journal Article
LanguageEnglish
Published 2012
Subjects
多态信息含量
平台
木豆
桑
测序
第二代
表达序列标签
转录组学
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Summary: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 as- sembly 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 posi- tions 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.
Bibliography:31-2013/Q
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 as- sembly 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 posi- tions 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.
Cajanus cajan （L.）; second-generation sequencing; transcriptome assembly; intron spanning region （ISR）markers.
ISSN:1674-2052
1752-9867