三个多倍体猕猴桃基因组Survey分析及系统进化研究  

Survey analysis and phylogenetic study of three polyploid kiwifruit ge-nomes

作　　者：周嘉 王飞飞 仲伟敏 齐勇 刘青 史斌斌 张晟 牛歆雨 郑乾明 唐冬梅 ZHOU Jia;WANG Feifei;ZHONG Weimin;QI Yong;LIU Qing;SHI Binbin;ZHANG Sheng;NIU Xinyu;ZHENG Qianming;TANG Dongmei(Guizhou Fruit Science Research Institute,Guizhou Academy of Agricultural Sciences,Guiyang 550006,Guizhou,China;College of Plant Sciences,Tibet Agricultural and Animal Husbandry College,Nyingchi 860000,Xizang,China)

机构地区：[1]贵州省农业科学院果树科学研究所,贵阳550006 [2]西藏农牧学院植物科学学院,西藏林芝860000

出　　处：《果树学报》2024年第11期2214-2223,共10页Journal of Fruit Science

基　　金：黔科合支撑[2023]一般045;黔果树所青年基金[2023]4号;国家现代农业产业技术体系项目(CARS-26);筑科合同[2023]2-3号;黔科合重大专项(字[2024]026)。

摘　　要：[目的]全面了解多倍体猕猴桃种质资源的染色体倍性和基因组特征,并分析其在猕猴桃属植物中的系统进化关系,以期为多倍体猕猴桃全基因组组装提供参考。[方法]基于流式细胞术分析中华猕猴桃AcD2301(Actinidia chinensis)、软枣猕猴桃AcD2302(Actinidia arguta)、对萼猕猴桃AcD2303(Actinidia valvata)染色体倍性,利用Illumina二代测序平台开展基因组Survey分析,并基于SNP构建15种猕猴桃属植物系统进化树。[结果]中华猕猴桃AcD2301、软枣猕猴桃AcD2302、对萼猕猴桃AcD2303的染色体倍性分别为四倍体、四倍体、六倍体,与survey分析结果一致。Kmer分析预测中华猕猴桃AcD2301、软枣猕猴桃AcD2302、对萼猕猴桃AcD2303单套基因组大小分别约为626 Mb、668 Mb、585 Mb,杂合度为3.00%、3.30%、8.06%,重复序列比例为43.70%、45.30%、40.70%。系统进化树显示软枣猕猴桃与对萼猕猴桃亲缘关系较近,且均从中华猕猴桃独立进化而来。[结论]分析了中华猕猴桃AcD2301、软枣猕猴桃AcD2302、对萼猕猴桃AcD2303的染色体倍性、基因组大小和系统进化关系,为将来开展多倍体猕猴桃全基因组测序提供了参考,也为深入研究猕猴桃多倍化和系统进化提供了理论支持。【Objective】Plant polyploidization is the evolution of adaption to environmental changes and protection of their own population development.The polyploidization of kiwifruit could double its chro-mosome number and affect the structure and function of its genome,thereby enriching the genetic diver-sity of the species.The study aimed to comprehensively understand the chromosomal ploidy and ge-nomic characteristics of polyploid kiwifruit germplasm resources,and analyze their systematic evolu-tionary relationships in kiwifruit.【Methods】This study analyzed the chromosome ploidy of AcD2301(Actinidia chinensis),AcD2302(A.arguta)and AcD2303(A.valvata)with reference to the diploid A.chinensis‘Hongyang’.The samples were analyzed by flow cytometry on the CyFlow Space flow cy-tometer after being lysed by CyStar UV Precise P kit and dyed by DAPI fluorescent dye in the dark.The total genomic DNA of kiwifruit was extracted by CTAB method,and then electrophoresis was con-ducted with 0.8%agarose gel.The DNA quality was detected with UV spectrophotometer.The second-generation sequencing technology Illumina NovaSeq sequencing platform was used to perform double end sequencing on the sample library.The softwares such as FastP were used to view the distribution of base quality,average error rate distribution of reads,and base content distribution of reads sequencing.The raw data with adapters and low-quality reads were filtered to obtain high-quality sequences,and the sequences were compared with nucleic acid databases.The high quality sequencing data was generated using Jellyfish(version 2.3.0)software k-mer19 to generate K-mer frequency tables,and genome size,heterozygosity,and repeatability were estimated using the GenomeScope 2.The next-generation se-quencing data of kiwifruit,published in the NGDC and NCBI databases,were compared with the refer-ence genome A.chinensis Hongyang v4.0.The SNP calling was performed using GATK software,and the Maximum likelihood algorithm in fast Tree software was used to construct phyloge

关 键 词：猕猴桃 基因组survey分析 基因组大小 系统进化 

分 类 号：S663.4[农业科学—果树学]