De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

Abstract Background Setaria italica is the second-most widely planted species of millets in world and an important model grain crop for research C4 photosynthesis abiotic stress tolerance. Through three genomes assembly annotation efforts, all were based on next generation sequencing technology, which limited genome continuity. Results Here we report a high-quality whole-genome new cultivar Huagu11, using single-molecule real-time High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total size Huagu11 was 408.37 Mb with scaffold N50 45.89 Mb. Compared other reported millet had highest genomic Intraspecies comparison showed about 94.97 94.66% Yugu1 genomes, respectively, able to be aligned as one-to-one blocks four inversion. contained approximately 19.43 Presence/absence Variation (PAV) 627 protein-coding transcripts, while 20.53 PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) 156,282 insertion-deletion (InDels) identified between these two genomes. should reflect genetic identity variation cultivars foxtail certain extent. Ser-626-Aln substitution acetohydroxy acid synthase ( AHAS ) found relative imazethapyr tolerance Huagu11. Conclusions A improved reference sequence assembled, intraspecies determined millet. Based sequence, it inferred that responsible will promote genic studies this beneficial improvement.