The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fr...The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.展开更多
旨在挖掘绵羊中与优异性状相关基因,对遗传改良与育种实践具有重要价值。本研究以93只策勒黑羊、33只皮山红羊和13只瓦格吉尔羊为对象,进行颈静脉采血、DNA提取、基因分型。用PLINK软件对基因型数据进行质量控制(质控标准为:剔除个体检...旨在挖掘绵羊中与优异性状相关基因,对遗传改良与育种实践具有重要价值。本研究以93只策勒黑羊、33只皮山红羊和13只瓦格吉尔羊为对象,进行颈静脉采血、DNA提取、基因分型。用PLINK软件对基因型数据进行质量控制(质控标准为:剔除个体检出率小于90%、SNP检出率小于95%、最小等位基因频率小于5%、哈代温伯格平衡P<1×10-6的SNPs)和主成分分析(PCA),构建进化树、群体祖先成分分析和连锁不平衡分析(LD),同时基于全基因组长纯合片段(runs of homozygosity,ROH)分析和群体遗传分化指数(F_(ST))分析,选择前10%的ROH片段作为高频区域和F_(ST)值的前5%位点作为受选择区域,参考绵羊基因组Oar_v4.0注释基因并进行GO和KEGG分析。F_(ST)和FROH结果表明,3个群体之间遗传分化水平较低,且在K=4呈现清晰的遗传背景分化。同时识别出ACVR1、ACVR1C、UPP2、CRY1和NR4A2等是南疆地方绵羊品种在干旱沙漠环境中形成遗传适应性的候选基因。本研究通过群体遗传结构多样性和选择信号分析,揭示了南疆地方绵羊品种的遗传变异特征,从多维度的遗传变异视角寻找到相关优异基因,为绵羊种质资源保护、新品种培育及资源多样性提升提供了重要参考依据。展开更多
基金supported by grants from the Agriculture Seed Improvement Projects of Shandong Province(Nos.2022LZGCQY010,2021ZLGX03,and 2021TSGC 1240)the China Agriculture Research System Project(No.CARS-49)。
文摘The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.
文摘旨在挖掘绵羊中与优异性状相关基因,对遗传改良与育种实践具有重要价值。本研究以93只策勒黑羊、33只皮山红羊和13只瓦格吉尔羊为对象,进行颈静脉采血、DNA提取、基因分型。用PLINK软件对基因型数据进行质量控制(质控标准为:剔除个体检出率小于90%、SNP检出率小于95%、最小等位基因频率小于5%、哈代温伯格平衡P<1×10-6的SNPs)和主成分分析(PCA),构建进化树、群体祖先成分分析和连锁不平衡分析(LD),同时基于全基因组长纯合片段(runs of homozygosity,ROH)分析和群体遗传分化指数(F_(ST))分析,选择前10%的ROH片段作为高频区域和F_(ST)值的前5%位点作为受选择区域,参考绵羊基因组Oar_v4.0注释基因并进行GO和KEGG分析。F_(ST)和FROH结果表明,3个群体之间遗传分化水平较低,且在K=4呈现清晰的遗传背景分化。同时识别出ACVR1、ACVR1C、UPP2、CRY1和NR4A2等是南疆地方绵羊品种在干旱沙漠环境中形成遗传适应性的候选基因。本研究通过群体遗传结构多样性和选择信号分析,揭示了南疆地方绵羊品种的遗传变异特征,从多维度的遗传变异视角寻找到相关优异基因,为绵羊种质资源保护、新品种培育及资源多样性提升提供了重要参考依据。
