Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Junpeng Shi,Jinsheng Lai,Minxuan Liu,Silong Sun,Weibin Song,Haiming Zhao,Xiangbo Zhang,Liangliang Huang,Wei Zhan,Yingsi Zhou,Lun Wang,Jihong Zhang,Xuxu Ma,Xiang Gao,Pinghua Li,Ping Lu

doi:10.1038/s41467-018-07876-6

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.

Highlights

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
There are 19,609 genes in foxtail millet that are syntenic with broomcorn millet, among which 16,884 (~86.2%) genes have two homologous copies retained in broomcorn millet, indicating rare gene loss after whole-genome duplication (WGD)
Phylogenetic analysis reveals a common ancestor before ~13.1 million years ago (Mya) between broomcorn millet and foxtail millet, and the tetraploidization is estimated to be happened within ~5.91 million years

Summary

Introduction

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. Broomcorn millet was a recent allotetraploid (2n = 4 × = 36) with its two subgenomes originated from two species closely related to P. capillare and P. repens[3,5] It could be used as a pioneer crop at marginal regions due to its short growing season (reaching maturity after ~60–90 days), extremely low water requirements, high salt tolerance, and nutrient resource usage efficiency[6,7]. Through a combination of PacBio sequencing, BioNano optical mapping and Hi-C (in vivo) mapping, we generate a chromosome scale assembly with a total scaffold length of ~848.4 Mb (N50 of ~8.24 Mb) that accounted for ~95.6% of the estimated genome size (~887.8 Mb). The genome sequence we report here is important to understand the dynamic evolution following genome tetraploidization in Paniceae, and benefit the molecular breeding of broomcorn millet in the future

Methods

Results

Conclusion