Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Junpeng Shi, Xuxu Ma, Jihong Zhang, Yingsi Zhou, Minxuan Liu, Liangliang Huang, Silong Sun, Xiangbo Zhang, Xiang Gao, Wei Zhan, Pinghua Li, Lun Wang, Ping Lu, Haiming Zhao, Weibin Song () and Jinsheng Lai ()
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Junpeng Shi: China Agricultural University
Xuxu Ma: China Agricultural University
Jihong Zhang: China Agricultural University
Yingsi Zhou: China Agricultural University
Minxuan Liu: Chinese Academy of Agricultural Sciences
Liangliang Huang: China Agricultural University
Silong Sun: China Agricultural University
Xiangbo Zhang: China Agricultural University
Xiang Gao: China Agricultural University
Wei Zhan: Annoroad Gene Technology (Beijing) Co., Ltd
Pinghua Li: Shandong Agricultural University
Lun Wang: Shanxi Academy of Agricultural Sciences
Ping Lu: Chinese Academy of Agricultural Sciences
Haiming Zhao: China Agricultural University
Weibin Song: China Agricultural University
Jinsheng Lai: China Agricultural University

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: Abstract Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.

Date: 2019
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DOI: 10.1038/s41467-018-07876-6

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