二倍体燕麦物种长穗燕麦的染色体水平基因组组装。

Chromosome-level genome assembly of the diploid oat species Avena longiglumis.

机构信息

State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.

South China National Botanical Garden, Guangzhou, China.

出版信息

Sci Data. 2024 Apr 22;11(1):412. doi: 10.1038/s41597-024-03248-6.

DOI:10.1038/s41597-024-03248-6

PMID:38649380

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11035610/

Abstract

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.

摘要

二倍体野生燕麦长穗燕麦具有营养价值和适应性特征，对普通燕麦（A. sativa）的育种很有价值。Illumina、Nanopore 和 Hi-C 数据的结合使我们能够组装出高质量的长穗燕麦染色体水平基因组（ALO），其组装大小为 3960.97Mb，组装 contig N50 为 12.68Mb，99% 的 BUSCO 完整性。共注释了 40845 个蛋白质编码基因。组装的基因组由 87.04%的重复 DNA 序列组成。与两个已发表的 ALO 基因组的基因组组装（PI657387）的点图比较表明，基因顺序的保守性和所有同源区在三个基因组组装中的相等扩展。在二倍体燕麦物种的基因组中，鉴定了两个最近的全基因组复制事件。这些发现为长穗燕麦的基因组特征提供了新知识，提供了有关物种多样性的信息，并将加速燕麦和相关谷物作物的功能基因组学和育种研究。