Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

Dubey, A and Farmer, A and Schlueter, J and Cannon, S B and Abernathy, B and Tuteja, R and Woodward, J and Shah, T and Mulasmanovic, B and Kudapa, H and Raju, N L and Gothalwal, R and Pande, S and Xiao, Y and Town, C D and Singh, N K and May, G D and Jackson, S and Varshney, R K (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Research, 18 (3). pp. 153-164. ISSN 1340-2838, 1756-1663

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Abstract

This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Cajanus cajan L.; next generation sequencing; transcriptome assembly; molecular markers; gene discovery
Agro Tags:	<b>Agrotags</b> - genes | genomes | genotypes | proteins | group communication | genetics | gene expression | dna | planting | crops <br><b>Fishtags</b> - NOT-AVAILABLE<br><b>Geopoliticaltags</b> - india | centre | act | mexico
Subjects:	Mandate crops > Pigeonpea
Depositing User:	Users 6 not found.
Date Deposited:	25 Jul 2011 11:47
Last Modified:	25 Jul 2011 11:49
URI:	http://oar.icrisat.org/id/eprint/111
Official URL:	http://dx.doi.org/doi:10.1093/dnares/dsr007
Projects:	UNSPECIFIED
Funders:	Generation Challenge Programme, Indian Council of Agricultural Research
Acknowledgement:	The authors are thankful to Dr Pawan Kulwal, Dr Punjabrao Deshmukh Krishi Vishwavidalaya, Akola (India), for providing the seeds of some genotypes used in this study.
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