Xiaoping Chen, Hongjie Li, Manish K. Pandey, Qingli Yang, Xiyin Wang, Vanika Garg, Haifen Li, Xiaoyuan Chi, Dadakhalandar Doddamani, Yanbin Hong, Hari Upadhyaya, Hui Guo, Aamir W. Khan, Fanghe Zhu, Xiaoyan Zhang, Lijuan Pan, Gary J. Pierce, Guiyuan Zhou, Katta A. V. S. Krishnamohan, Mingna Chen, Ni Zhong, Gaurav Agarwal, Shuanzhu Li, Annapurna Chitikineni, Guo-Qiang Zhang, Shivali Sharma, Na Chen, Haiyan Liu, Pasupuleti Janila, Shaoxiong Li, Min Wang, Tong Wang, Jie Sun, Xingyu Li, Chunyan Li, Mian Wang, Lina Yu, Shijie Wen, Sube Singh, Zhen Yang, Jinming Zhao, Chushu Zhang, Yue Yu, Jie Bi, Xiaojun Zhang, Zhong-Jian Liu, Andrew H. Paterson, Shuping Wang, Xuanqiang Liang, Rajeev K. Varshney, and Shanlin Yu

Significance

We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, providing details on total genes present in the genome. Genome analysis suggests that the peanut lineage was affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion since their formation by human hands. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants. This study also provides millions of structural variations that can be used as genetic markers for the development of improved peanut varieties through genomics-assisted breeding.

Abstract

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

See: http://www.pnas.org/content/113/24/6785.abstract.html?etoc

PNAS June 14 2016; vol.113; no.24: 6785–6790

Fig. 1.

A. duranensis genome overview. From the outer edge inward, circles represent the 50 largest DNA sequence scaffolds (green), the genes on each scaffold (purple), SNP density at 100-kb intervals (blue), repeat density at 100 kb (green), transposable element density at 100 kb (yellow), and the fold-change values of transcripts (red). Links in the core connect duplicated sets of genes (E-value threshold of <1e-10 and 85% similarity).