Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

First author: Junpeng Shi; Affiliations: China Agricultural University (中国农业大学): Beijing, China

Corresponding author: Jinsheng Lai

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.

糜子具有非常强的非生物胁迫抗性，并且可能是最早被驯化的作物，栽培历史最早可追溯到大约一万年前。作者通过整合PacBio测序、BioNano光学图谱以及Hi-C图谱构建了糜子基因组。其中，18个scaffold占了糜子基因组的95.6%。作者在糜子四倍体基因组上共注释了63671个蛋白编码基因。谷子中86.2%的共线性基因在糜子中均有两个同源拷贝，说明在糜子基因组四倍化之后基因丢失较少。系统发育分析显示糜子和谷子大约在13.1个百万年前分化，糜子基因组的四倍化大约发生在5.91个百万年前。本文报道的基因组不仅有利于糜子育种，对于其它的黍属物种也具有非常重要的参考价值。

通讯：赖锦盛 (http://cab.cau.edu.cn/art/2017/6/9/art_27218_60.html)

个人简介：1987-1991年，福建农学院，学士；1991-1993年，北京农业大学，农学院植物遗传育种系硕士；1993-1996年，中国农业大学，农学院植物遗传育种系博士；1996-1999年，美国新泽西州立大学，Waksman研究所博士后。

研究方向：玉米基因组学；玉米籽粒发育遗传调控；玉米胚乳基因印迹；玉米基因工程和分子育种。

doi: https://doi.org/10.1038/s41467-018-07876-6

Journal: Nature Communications

First Published: January 25, 2019