Abstract
BackgroundSetaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity.ResultsHere we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11.ConclusionsA new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
Highlights
Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance
Compared with the other three reported millet genomes, the Huagu11 genome has the minimum number of contigs and the longest contig N50 length, which indicates the highest genomic continuity (Table 1; Table S5)
A new improved high-quality reference genome sequence of Setaria italica was assembled based on Single-molecule real-time sequencing (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies
Summary
Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Foxtail millet (Setaria italic) is a climate-resilient cereal crop domesticated in northern China more than 8000 years ago [1] and is mainly cultivated in arid and semi-arid regions. It serves as a model crop for the study of C4 photosynthesis, stress tolerance and bioenergy traits, due to its small genome size and short lifecycle [2,3,4,5,6]. The ‘Yugu1’ genome assembly based on Sanger sequencing, has higher contiguity than the short-read genome assembly of ‘Zhang gu’ (contig N50: 126.3 kb versus 25.8 kb) and is currently used as a reference genome of foxtail millet. As quantitative genetic analyses have revealed that many causal variations underlying phenotype changes are from regulatory regions, a complete and high-quality genome assembly is crucial to understand of the genetic mechanisms of climate-resilient features, genome evolution and important agronomic traits in foxtail millet
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