SynDiv:An efficient tool for chromosome collinearity-based population genomics analyses  

作　　者：Ze-Zhen Du Jia-Bao He Wen-Biao Jiao 

机构地区：[1]National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops,Huazhong Agricultural University,Wuhan 430070,China [2]Hubei Hongshan Laboratory,Wuhan 430070,China [3]Hubei Key Laboratory of Agricultural Bioinformatics,College of Informatics,Huazhong Agricultural University,Wuhan 430070,China

出　　处：《Plant Communications》2024年第12期5-8,共4页植物通讯(英文)

基　　金：National Natural Science Foundation of China(no.32270685);National Natural Science Fund for Excellent Young Scientists Fund Program(Overseas);"Young Scientist Fostering Funds for the National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops."

摘　　要：Dear Editor,The advancement of long-read sequencing technologies has significantly enhanced pan-genome studies,enabling numerous chromosome-level de novo assemblies for a single species(Jiao and Schneeberger,2017;Marks et al.,2021;Shi et al.,2023;Xie et al.,2024).These population-scale assembly comparisons have revealed numerous structural variations(SVs),many of which are causal for important traits(Shi et al.,2023).However,traditional population genetic analyses,which primarily focus on SNP markers,often overlook these rearranged or non-collinear regions.To analyze the evolutionary characteristics of these regions and quantify the conservation of genome collinearity at the population level,we previously introduced a parameter called synteny diversityπsyn(Jiao and Schneeberger,2020).Unlike nucleotide diversity,which measures average sequence differences,πsyn quantifies the degree of collinearity between individual genomes within a population.However,calculatingπsyn involves pairwise alignment between genomes,resulting in a computational time complexity of O((n^(2)+n)/2).In our previous study,calculating this parameter for a small Arabidopsis thaliana(A.thaliana)population with eight genomes required dozens of hours.

关 键 词：TRAITS CALCULATING ALIGNMENT 

分 类 号：Q94[生物学—植物学]