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

This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. Roche FLX/454 sequencing was 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 127,754 transcript assemblies (TAs). Functional analysis of these TAs highlights several active pathways and processes in the sampled tissues. Comparison of the TAs with the soybean genome showed similarity to between 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 TAs and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8,137 simple sequence repeats (SSRs), 12,141 single nucleotide polymorphisms (SNPs) and 5,845 intron spanning regions (ISRs). 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.