两个二倍体和一个自四倍体青钱柳基因组的组装。

Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes.

机构信息

Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing, 210037, China.

Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.

出版信息

Sci Data. 2023 Aug 2;10(1):507. doi: 10.1038/s41597-023-02402-w.

DOI:10.1038/s41597-023-02402-w

PMID:37532689

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10397226/

Abstract

Cyclocarya paliurus, an endemic species in the genus Juglandaceae with the character of heterodichogamy, is one of triterpene-rich medicinal plants in China. To uncover the genetic mechanisms behind the special characteristics, we sequenced the genomes of two diploid (protandry, PA-dip and protogyny, PG-dip) and one auto-tetraploid (PA-tetra) C. paliurus genomes. Based on 134.9 (~~225x), 75.5 (~~125x) and 271.8 Gb (226x) subreads of PacBio platform sequencing data, we assembled 586.62 Mb (contig N50 = 1.9 Mb), 583.45 Mb (contig N50 = 1.4 Mb), and 2.38 Gb (contig N50 = 430.9 kb) for PA-dip, PG-dip and PA-tetra genome, respectively. Furthermore, 543.53, 553.87, and 2168.65 Mb in PA-dip, PG-dip, and PA-tetra, were respectively anchored to 16, 16, and 64 pseudo-chromosomes using over 65.4 Gb (109x), 68 Gb (~~113x), and 264 (~~220x) Hi-C sequencing data. Annotation of PA-dip, PG-dip, and PA-tetra genome assembly identified 34,699, 35,221, and 34,633 protein-coding genes (90,752 gene models) or allele-defined genes, respectively. In addition, 45 accessions from nine locations were re-sequenced, and more than 10 × coverage reads were generated.

摘要

青钱柳是胡桃科青钱柳属的特有种，具有雌雄异熟的特点，是中国富含三萜类化合物的药用植物之一。为了揭示其特殊特征的遗传机制，我们对两个二倍体（先雄型，PA-dip 和先雌型，PG-dip）和一个自四倍体（PA-tetra）青钱柳基因组进行了测序。基于 134.9（~~225x）、75.5（~~125x）和 271.8 Gb（226x）的 PacBio 平台测序数据的亚读数，我们组装了 586.62 Mb（contig N50 = 1.9 Mb）、583.45 Mb（contig N50 = 1.4 Mb）和 2.38 Gb（contig N50 = 430.9 kb）的 PA-dip、PG-dip 和 PA-tetra 基因组，分别。此外，在 PA-dip、PG-dip 和 PA-tetra 中，分别有 543.53、553.87 和 2168.65 Mb 被锚定到 16、16 和 64 个假染色体上，使用了超过 65.4 Gb（109x）、68 Gb（~~113x）和 264（~~220x）Hi-C 测序数据。PA-dip、PG-dip 和 PA-tetra 基因组组装的注释分别鉴定了 34699、35221 和 34633 个蛋白质编码基因（90752 个基因模型）或等位基因定义基因。此外，对来自九个地点的 45 个样本进行了重新测序，生成了超过 10×的覆盖读数。