基于流式细胞术和基因组Survey检测黄连木基因组大小  

Estimation of Genome Sizes of Pistacia chinensis by Flow Cytometry and Genome Survey

作　　者：周美君 尹月 张永洪[1] ZHOU Mei-jun;YIN Yue;ZHANG Yong-hong(College of Life Science,Yunnan Normal University,Kunming 650500,Yunnan China)

机构地区：[1]云南师范大学生命科学学院,云南昆明650500

出　　处：《亚热带植物科学》2024年第6期495-502,共8页Subtropical Plant Science

基　　金：国家自然科学基金(31760048)。

摘　　要：为确定黄连木Pistacia chinensis全基因组测序策略,采用流式细胞术结合高通量测序技术对黄连木基因组大小进行检测。结果表明:(1)以番茄Solanumlycopersicum和拟南芥Arabidopsisthaliana为内参,通过流式细胞术估算黄连木基因组大小分别约为480 Mb和406 Mb;(2)从高通量测序获得86 Gb原始数据,过滤处理后得到约85 Gb有效数据;(3)通过将测序数据与NT库进行比对,发现前五个匹配数量最多的物种均为漆树科物种,在这些物种中,黄连木与同属的阿月浑子P.vera序列相似度最高,测序数据不存在外源污染;(4)K-mer分析显示黄连木基因组大小为418Mb,杂合度达1.89%,重复序列比例为57.5%。综上,黄连木基因组属于高杂合度高重复率的复杂基因组,建议使用Pacbio三代测序技术结合Hi-C测序技术的组装策略,同时重视杂合区域的组装。该研究结果为黄连木全基因组学研究提供参考和重要的数据指导。Pistacia chinensis,a deciduous tree of the genus Pistacia(Anacardiaceae),is an important oil plant resource for its seeds being rich in oil.It has value in wood production and landscape too.Until now,no relevant information on the whole genome of P.chinensis has been found,which limits its resource utilization and germplasm innovation.To determine the whole genome sequencing strategy of P.chinensis,flow cytometry combined with high-throughput sequencing technology was employed to estimate the genome size of this species.The results were as follows:(1)The genome sizes of P.chinensis were estimated to be approximately 480 Mb and 406 Mb by flow cytometry using Solanum lycopersicum and Arabidopsis thaliana as internal references,respectively.(2)86 Gb of raw data were produced in next-generation sequencing and approximately 85 Gb of clean data were obtained after filtering.(3)NT database comparison found no exogenous pollution in the sequencing data,with five most math species belonging to Anacardiaceae.Pistacia vera,a congeneric species,had the highest sequence similarity with P.chinensis.(4)K-mer analysis showed that the genome size of P.chinensis was 418 Mb with a heterozygosity level of 1.89%and repetitive sequences ratio of 57.5%.The results revealed that the genome of P.chinensis was a complex genome with high heterozygosity and repetitive rates.It is recommended to combine PacBio sequencing technology and Hi-C sequencing in genome assembling with specific concern on heterozygous regions.This study provides valuable reference and important database for the genomics of P.chinensis.

关 键 词：黄连木 基因组Survey分析 流式细胞术 K-mer分析 基因组大小 

分 类 号：Q943[生物学—植物学]