四倍体油茶树（Camellia meiocarpa Hu）的单倍型解析基因组组装

Haplotype-resolved genome assembly of the tetraploid Youcha tree Camellia meiocarpa Hu.

作者信息

Wang Rui, Li Weiguo, He Zhilong, Lyu Haomin, Wang Xiangnan, Ye Changrong, Xun Chengfeng, Xiao Gaohong, Zhang Ying, Zhang Zhen, Ma Yushen, Chen Longsheng, Chen Bolin, Jia Gaofeng, Tian Bingchuan, Chen Yongzhong

机构信息

Research Institute of Youcha, Hunan Academy of Forestry, Changsha, China.

National Engineering Research Center of Youcha, Changsha, China.

出版信息

Sci Data. 2025 Mar 31;12(1):541. doi: 10.1038/s41597-025-04887-z.

DOI:10.1038/s41597-025-04887-z

PMID:40164616

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11958635/

Abstract

Camellia meiocarpa Hu, a member of Youcha species in the genus Camellia, is an important woody edible Youcha plant with high ecological and economic value. The haplotype-resolved genome assembly of this tetraploid species can shed light on genomic evolution and the functional divergence among subgenomes and haplotypes. In this study, we achieved the first chromosome-level haplotype-resolved genome assembly using PacBio HiFi, Hi-C, and Illumina sequencing. The scaffolds, with an N50 of 44.46 Mb and 41.40 Mb, were mapped to 60 chromosomes and four distinct haplotypes, each with unique transposon features. The haplotypes varied in length (2967.25 Mb to 3041.66 Mb) and contained 51,336 to 52,631 protein-coding genes, 99.4% of which were annotated. Non-coding RNAs and repetitive elements were identified across haplotypes. This comprehensive genomic resource will enhance molecular and genetic studies, aiding in the conservation and utilization of Youcha.

摘要

油茶（Camellia meiocarpa Hu）是山茶属攸茶组的成员，是一种具有重要生态和经济价值的木本可食用油茶植物。对这个四倍体物种进行单倍型解析的基因组组装，有助于了解基因组进化以及亚基因组和单倍型之间的功能差异。在本研究中，我们利用PacBio HiFi、Hi-C和Illumina测序技术，首次完成了染色体水平的单倍型解析基因组组装。支架的N50分别为44.46 Mb和41.40 Mb，被定位到60条染色体和4个不同的单倍型上，每个单倍型都有独特的转座子特征。单倍型长度不同（2967.25 Mb至3041.66 Mb），包含51,336至52,631个蛋白质编码基因，其中99.4%得到注释。在单倍型中鉴定出了非编码RNA和重复元件。这一全面的基因组资源将加强分子和遗传研究，有助于攸茶的保护和利用。