帝汶蟹草(Digitaria radicosa)染色体组规模的基因组组装:Poaceae 的有用基因组资源。

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-10-10 DOI:10.1093/g3journal/jkae242
Koki Minoji, Toshiyuki Sakai
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引用次数: 0

摘要

帝汶蟹草(Digitaria radicosa)是一种常见于东南亚和大洋洲的草种。Digitaria物种具有很高的种内和种间遗传和表型多样性,这表明其作为遗传资源的潜在用途。然而,由于目前唯一的高质量参考基因组是针对四倍体Digitaria物种的,因此二倍体物种D. radicosa的参考基因组将成为Digitaria和Poaceae植物基因组研究的有用资源。在此,我们介绍了 D. radicosa 的染色体级基因组组装,并描述了其遗传特征;我们还说明了其作为 Poaceae 植物基因组资源的有用性。我们利用 PacBio HiFi 长读数构建了一个 441.6 Mb 的组装草案,其中包括 61 个等位基因,N50 等位基因长度为 41.5 Mb。我们预测了 26,577 个蛋白编码基因,BUSCO 得分为 96.5%。为了证明D. radicosa参考基因组的实用性,我们基于新的参考基因组研究了Digitaria物种的进化和日本Digitaria植物的遗传多样性。我们还确定了D. radicosa与两种菊科作物(芋和稻)之间的同源区块,以及D. radicosa中代表性抗性基因的多样化分布。这里介绍的 D. radicosa 参考基因组有助于阐明 Digitaria 物种的遗传亲缘关系和 Digitaria 植物的遗传多样性。此外,D. radicosa 基因组还将成为 Poaceae 基因组学和作物育种的重要基因组资源。
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A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae.

Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6 Mb draft assembly consisting of 61 contigs with an N50 contig length of 41.5 Mb, using PacBio HiFi long reads. We predicted 26,577 protein-coding genes, reaching a BUSCO score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and 2 Poaceae crops, fonio and rice, and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.

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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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