Abstract
Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance. We report a chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing and Hi-C technologies. The 2.07-Gb assembly covers 96.64% of the genome, with contig N50 of 1.71 Mb. The centromere and telomere sequences are assembled for all 19 chromosomes and chromosome 10, respectively. Allotetraploid origin of the M. lutarioriparius is confirmed using centromeric satellite repeats. The tetraploid genome structure and several chromosomal rearrangements relative to sorghum are clearly demonstrated. Tandem duplicate genes of M. lutarioriparius are functional enriched not only in terms related to stress response, but cell wall biosynthesis. Gene families related to disease resistance, cell wall biosynthesis and metal ion transport are greatly expanded and evolved. The expansion of these families may be an important genomic basis for the enhancement of remarkable traits of M. lutarioriparius.
Highlights
Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance
The accessions we investigated were divided into three distinct groups, one group containing the accessions from M. sinensis (Type I and II), M. sacchariflorus (Type I), M. transmorrisonensis, and M. floridulus, one group containing the accessions from M. lutarioripairus, M. sacchariflorus (Type II), and M. × giganteus and another group containing the accessions from M. capensis, M. junceus, and S. spontaneum (Fig. 5)
Here, we generated a qualified chromosome-scale assembly of the M. lutarioriparius genome using the long reads generated by Oxford Nanopore Technologies and high-throughput chromosome conformation capture (Hi-C) technology
Summary
Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance. Gene families related to disease resistance, cell wall biosynthesis and metal ion transport are greatly expanded and evolved The expansion of these families may be an important genomic basis for the enhancement of remarkable traits of M. lutarioriparius. It is a rhizomatous perennial plant that has great potential for bioenergy production for its high biomass yield and strong stress tolerance[1]. It is one of a few C4 photosynthetic plants that adapt to the cold conditions, which makes Miscanthus a valuable genetic resource for sugarcane cold tolerance breeding[1,3]. Features Number of scaffolds Total size of scaffolds Longest scaffold Shortest scaffold Mean scaffold size Median scaffold size N50 scaffold length L50 scaffold count Scaffold GC content Scaffold N content Percentage of assembly in scaffolded contigs Average number of contigs per scaffold BUSCO (complete) LTR Assembly Index (LAI)
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