The genome of broomcorn millet

Abstract

Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C₄ subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C₄ biology.

Fig. 1

Synteny and distribution of features in the broomcorn millet genome. The number and length (Mb) of pseudochromosomes are indicated outside of the ring. a TE coverage, b gene density, c average transcript levels, d marker density represented by the number of SNPs and e GC (guanine-cytosine) content of the genome in 1-Mb nonoverlapping windows. f Synteny blocks >1 Mb long among homologous broomcorn millet chromosomes are indicated. TE transposable elements, SNP single nucleotide polymorphism .

Fig. 2

Evolutionary analyses of the broomcorn millet genome. a Species phylogenetic tree constructed from single-copy orthologs. Lineage divergence time is indicated at each branch point. The photosynthesis type of each species is indicated by colored dots at each node. b 4DTv distance of homologs genes from broomcorn millet (Pm) and foxtail millet (Si). c Synteny blocks identified between broomcorn millet and foxtail millet, and between broomcorn millet and sorghum (Sb). Only synteny blocks >0.5 Mb long are shown.

Fig. 3

Comparative genomics of gene families in broomcorn millet. a The number of gene families that expanded or contracted during evolution mapped to the species phylogenetic tree. b Overlap of gene families in broomcorn millet (P. miliaceum) and four other grasses. c Gene copy number and domain architecture of BTB proteins in broomcorn millet (Pm), foxtail millet (Si), rice (Os), and Arabidopsis thaliana (At). Gene copy numbers that are at least twofold higher in broomcorn millet (P. miliaceum) than in other species are labeled red. BTB broad complex/tramtrack/bric-a-brac, NPH3 nonphototropic-hypocotyl 3, MATH meprin-and-TRAF-homology, BACK BTB and C-terminal Kelch, TAZ Transcription Adaptor putative Zinc finger, TPR Tetratricopeptide repeat, F5_F8 type C discoidin domain.

Fig. 4

A proposed model of C₄ photosynthesis in broomcorn millet. a Diagram depicting the main proteins and metabolic fluxes involved in C₄ photosynthesis. Proteins are colored based on traditional models: the ones that commonly function in NAD-ME and NADP-ME C₄ are in blue; the ones that participate in NAD-ME C₄ are in magenta; the ones that participate in NADP-ME C₄ are in green. Abbreviations for metabolites and enzymes: CO₂ carbon dioxide, Ala alanine, Asp aspartate, Mal malate, Pyr pyruvate, OAA oxaloacetate, PEP phosphoenolpyruvate, CA carbonic anhydrase, PEPC phosphoenolpyruvate carboxylase, PPDK pyruvate/orthophosphate dikinase, AspAT aspartate aminotransferase, AlaAT alanine aminotransferase, NADP-MDH NADP-dependent malate dehydrogenase, NADP-ME NADP-dependent malic enzyme, NAD-MDH NAD-dependent malate dehydrogenase, NAD-ME NAD-dependent malic enzyme, PEPC-K PEPC kinase, PEP-CK phosphoenolpyruvate carboxykinase. Metabolite transporters are presented by circled numbers or question marks on the membrane: 1, plasma membrane intrinsic protein (PIP); 2, dicarboxylate transporter 1 (DiT1); 3, phosphate/phosphoenolpyruvate translocator (PPT); 4, sodium bile acid symporter 2 (BASS2) and sodium: hydrogen antiporter (NHD); 5, malate phosphate antiport 1 (DIC1); 6, dicarboxylate transporter 2 (DiT2); 7, Mitochondrial pyruvate carrier. b–d Synteny blocks containing b CA, c NAD-ME and d NADP-ME genes. Chromosomes or scaffolds are shown as rectangular boxes, which are not drawn to scale. Synteny blocks are shaded gray with red lines indicating the position of genes. The species are labeled as follows: Pm = broomcorn millet, Si = foxtail millet, Sb = sorghum, Do = Dichanthelium oligosanthes, Os = rice. e Heatmap showing the expression level of candidate genes involved in C₄ carbon fixation in photosynthetic and nonphotosynthetic tissues of broomcorn millet.