Sequencing Pigeonpea Genome

Abstract

Availability of draft genome has brought quantum jump in pigeonpea status and facilitated to move it to the league of genomic resource rich crops. It is important to mention that pigeonpea became the first orphan and non-industrial grain legume in 2012 to have the draft genome sequence. An elite pigeonpea genotype Asha (ICPL 87119) was used to develop the draft genome in two different sequencing efforts. The pigeonpea genome sequence effort led by International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) used Illumina Genome Analyzer and HiSeq 2000 NGS platform, and a total of 237.2 Gb of sequence was generated. De-novo genome assembly combined with Sanger-based bacterial artificial chromosome end sequences and a genetic map was used to assemble raw reads into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes with an average transcript length of 2348 bp, coding-sequence size of 959.35 bp and 3.59 exons per gene. Analysis of genome assembly for repetitive DNA showed presence of transposable elements (TEs) in 49.61% of assembled genome. The pigeonpea genome sequencing led by National Research Centre on Plant Biotechnology (NRCPB) used 454 GS-FLX sequencing chemistry, with mean read lengths of >550 bp and >10-fold genome coverage, was used to assemble ~511 Mb sequence data. In this study, 47,004 protein-coding genes were predicted. This study also reported 1213 disease resistance/defense response genes and 152 abiotic stress tolerance genes. The available pigeonpea draft genome information is expected to facilitate genomics-assisted breeding for the targeted traits that could improve food security in many developing countries.