ArticleBMC plant biology2021
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.
Article in BMC plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 22 citations in OpenAlex.
- Modern genomic and omics-based technologies for millet breeding and genetic improvement.Frontiers in plant science · 2026Review
- Genome-wide identification of the WIP family in foxtail millet (Setaria italica) and functional analysis of SiWIP3 in inhibiting growth in transgenic Arabidopsis thaliana.BMC genomics · 2025Article
- Tissue-Specific Expression Analysis and Functional Validation ofPlants (Basel, Switzerland) · 2025Article
- Genomic resources, opportunities, and prospects for accelerated improvement of millets.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.).Functional & integrative genomics · 2023Article
- Comparatively Evolution and Expression Analysis of GRF Transcription Factor Genes in Seven Plant Species.Plants (Basel, Switzerland) · 2023Article
- MDSi: Multi-omics Database for Setaria italica.BMC plant biology · 2023Article
- GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events.Plant physiology · 2022Article
- Comparative metabolomic and transcriptomic analysis reveals a coexpression network of the carotenoid metabolism pathway in the panicle of Setaria italica.BMC plant biology · 2022Article
- Multi-omics intervention inFrontiers in plant science · 2022Review
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12 authors at 3 institutions in 1 country.
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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.
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