大岛樱（Cerasus speciosa）的近乎完整基因组组装

A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa.

作者信息

Fujiwara Kazumichi, Toyoda Atsushi, Biswa Bhim B, Kishida Takushi, Tsuruta Momi, Nakamura Yasukazu, Kimura Noriko, Kawamoto Shoko, Sato Yutaka, Katsuki Toshio, Koide Tsuyoshi

机构信息

Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan.

Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.

出版信息

Sci Data. 2025 Feb 4;12(1):162. doi: 10.1038/s41597-025-04388-z.

DOI:10.1038/s41597-025-04388-z

PMID:39905005

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11794698/

Abstract

The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth "Sakurakkabu" tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.

摘要

大岛樱（Cerasus speciosa）原产于日本，具有重要的文化和园艺价值。在本研究中，我们展示了一个来自伊豆大岛老龄“樱之果”树的大岛樱端粒到端粒的近乎完整的基因组组装。利用Illumina短读长、PacBio长读长和Hi-C测序技术，我们构建了一个269.3 Mbp的基因组组装，其重叠群N50为32.0 Mbp。我们研究了组装基因组中重复序列的分布，并确定了疑似着丝粒的区域。对这些假定着丝粒区域的详细结构分析表明，大岛樱的着丝粒区域由单体长度为166或167 bp的重复序列组成。与广义李属基因组的比较基因组分析揭示了结构变异和保守的共线性区域。这个高质量的参考基因组为研究樱属物种的遗传多样性和进化历史提供了关键工具，有助于园艺研究的进展和这一标志性物种的保护。