Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

IF 3.9 2区生物学 Q1 GENETICS & HEREDITY

DNA Research Pub Date : 2023-02-01 DOI:10.1093/dnares/dsac052

Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Isobe

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引用次数: 3

Abstract

Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of 'Takanotsume'. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3,058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34,324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e. chromosomal rearrangements and transposon-insertion polymorphisms) between 'Takanotsume' and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of 'Takanotsume'.

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日本地方辣椒品种辣椒的染色体规模基因组组装。

在这里，我们报告了一种流行的日本辣椒地方品种辣椒的基因组序列，辣椒年'Takanotsume。我们利用长读测序和光学定位技术，结合遗传定位技术，获得了‘Takanotsume’染色体尺度的基因组组装。该组装体由12个伪分子组成，与C. annuum的基本染色体数目相对应，大小为3058.5 Mb，占估计基因组大小的97.0%。在基因组中共预测到34,324个高置信度基因，83.4%的基因组组装被重复序列占据。对两个辣椒系的链读测序衍生的从头基因组组装的比较基因组学分析和辣椒物种的全基因组重测序分析揭示了“Takanotsume”与其亲缘种之间不仅核苷酸序列存在差异，而且基因组结构(即染色体重排和转座子插入多态性)也存在差异。总的来说，本研究获得的基因组序列数据将加速辣椒的泛基因组学和育种，并有助于剖析辣椒重要农学性状的遗传机制。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

DNA Research 生物-遗传学

CiteScore

6.00

自引率

4.90%

发文量

审稿时长

4.5 months

期刊介绍： DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Comprehensive analysis of the functions of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes, gene families and genomes, 4) Computer algorithms and/or their applications relevant to structural and functional analysis of genes and genomes. The journal also welcomes novel findings in other scientific disciplines related to genomes.