红树莓(Rubus idaeus L.)的高质量基因组测序和分析

Haopeng Zhang, Weihua Li, Guodong Li, Jiaren Liu, Hongsheng Chen, Chunpeng Zhang, Jinlu Zhao, Zhicheng Zhang, Qiang Lv, Yan Zhang, Guohui Yang, Ming Liu
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引用次数: 0

摘要

红树莓(Rubus idaeus L.)属于蔷薇科水果作物,是人类健康的重要营养来源。在此,我们利用太平洋生物科学公司的单分子实时(SMRT)测序和高通量染色体构象捕获(Hi-C)测序技术组装了基因组,并报告了一个高质量的红树莓基因组(DNS-1),该基因组有321.29 Mb,组装成7条染色体。DNS-1 基因组的 LAI 得分为 21.32,属于黄金质量。约52.3%的组装序列被注释为重复序列,24.15%由长末端重复元件组成。DNS-1共预测了29814个编码蛋白质的基因和2474个假基因。我们对 DNS-1 的完整基因组进行了鉴定,并将其与其他七个物种的基因组进行了比较。我们发现,有 652 个基因家族是 DNS-1 所独有的,它们是由一个祖先形成的。在 DNS-1 基因组中,分别有 1000 和 5193 个基因家族发生了扩展和收缩。该基因组可用于了解蔷薇科植物基因组的结构和进化,并可用于鉴定控制重要性状的基因和改进育种工作。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

The High-Quality Genome Sequencing and Analysis of Red Raspberry (Rubus idaeus L.)

The High-Quality Genome Sequencing and Analysis of Red Raspberry (Rubus idaeus L.)

Red raspberry (Rubus idaeus L.), which is an important nutritional source for human health, belongs to fruit crops of the Rosaceae family. Here, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to assemble genomes and reported a high-quality Rubus idaeus L. (DNS-1) genome with 321.29 Mb assembled into seven chromosomes. The LAI score of the DNS-1 genome assembly was 21.32, belonging to gold quality. Approximately 52.3% of the assembly sequences were annotated as repetitive sequences, and 24.15% were composed of long terminal repeat elements. A total of 29,814 protein-coding genes and 2474 pseudogenes were predicted in DNS-1. We characterized the complete genomes of DNS-1 and compared them to those of seven other species. We found that 652 gene families were unique to DNS-1 and they were shaped from an ancestor. There were 1000 and 5193 gene families that expanded and contracted in the DNS-1 genome. The Rubus idaeus L. genome can be used to understand the structure and evolution of Rosaceae genomes and can be developed to identify genes controlling important traits and improve breeding work.

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Comparative and Functional Genomics
Comparative and Functional Genomics 生物-生化与分子生物学
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