Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena, Jessica A Schlueter, Mark T A Donoghue, Sarwar Azam, Guangyi Fan, Adam M Whaley, Andrew D Farmer, Jaime Sheridan, Aiko Iwata, Reetu Tuteja, R Varma Penmetsa, Wei Wu, Hari D Upadhyaya, Shiaw-Pyng Yang, Trushar Shah, K B Saxena, Todd Michael, W Richard McCombie, Bicheng Yang, Gengyun Zhang, Huanming Yang, Jun Wang, Charles Spillane, Douglas R Cook, Gregory D May, Xun Xu, Scott A Jackson

Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.