两个栽培枣品种的染色体水平基因组组装。

Chromosome-level genome assembly of two cultivated Jujubes.

机构信息

Institute of Horticulture, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China.

出版信息

Sci Data. 2024 Oct 17;11(1):1144. doi: 10.1038/s41597-024-03992-9.

DOI:10.1038/s41597-024-03992-9

PMID:39420037

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11486999/

Abstract

Jujube (Ziziphus jujuba Mill.) is a valuable tree species with economic, edible, medicinal, and ecological conservation benefits. In this study, we used PacBio HiFi sequencing and Hi-C technology to assemble chromosome-level genomes of two cultivated Jujubes, namely 'Lingwuchangzao' and 'Shiguang'. The genome sizes of 'Lingwuchangzao' and 'Shiguang' were 385.66 Mb and 394.12 Mb, respectively, with contig N50 sizes of 30.62 Mb and 4.30 Mb. These genomes contained 31,082 and 31,015 protein-coding genes, with repeat element contents of 42.11% and 42.33%, respectively. Phylogenetic analysis revealed that 'Lingwuchangzao' was sister to 'Shiguang' and followed by 'Dongzao'. Additionally, comparative analysis of gene families among 'Lingwuchangzao', 'Shiguang', 'Dongzao', 'Junzao', and 'Suanzao' identified 15,988 (57.98%) core gene families, 11,191 (40.59%) disposable gene families, and 394 (1.43%) private gene families. Overall, the assembly of the genomes of these two cultivated Jujube varieties provides valuable genetic information for Jujube evolution, functional genomics research, and molecular breeding.

摘要

枣（Ziziphus jujuba Mill.）是一种具有经济、食用、药用和生态保护价值的珍贵树种。本研究利用 PacBio HiFi 测序和 Hi-C 技术组装了两个栽培枣品种‘灵乌早’和‘石光’的染色体水平基因组。‘灵乌早’和‘石光’的基因组大小分别为 385.66 Mb 和 394.12 Mb，contig N50 大小分别为 30.62 Mb 和 4.30 Mb。这些基因组包含 31,082 个和 31,015 个蛋白质编码基因，重复元件含量分别为 42.11%和 42.33%。系统发育分析表明，‘灵乌早’与‘石光’亲缘关系最近，其次是‘冬枣’。此外，对‘灵乌早’、‘石光’、‘冬枣’、‘骏枣’和‘酸枣’之间基因家族的比较分析鉴定出 15,988 个（57.98%）核心基因家族、11,191 个（40.59%）可丢弃基因家族和 394 个（1.43%）专性基因家族。总之，这两个栽培枣品种基因组的组装为枣进化、功能基因组学研究和分子育种提供了有价值的遗传信息。