Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hem...Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hemisphere forests,and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations.Here we used a newly sequenced genome of Quercus gilva,an evergreen oak species from East Asia,with 18 published Fagales genomes to determine how Fagaceae genomes have evolved,identify genomic footprints of ecological adaptability in oaks in general,as well as between evergreen and deciduous oaks.We found that oak species exhibited a higher degree of genomic conservation and stability,as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events.In addition,we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense(e.g.,cuticle biosynthesis and oxidosqualene cyclase genes),which may represent the foundation for the ecological adaptation of oak species.Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks.This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic,genome evolutionary,and functional genomic analyses.展开更多
饭甑青冈(Cyclobalanopsis fleuryi)是中国及越南的常绿树种,具有重要的经济和药用价值。该研究以饭甑青冈叶片为材料,通过Illumina HiSeq X ten高通量测序平台,对其叶绿体基因组进行测序、组装和注释。结果表明,饭甑青冈叶绿体全基因...饭甑青冈(Cyclobalanopsis fleuryi)是中国及越南的常绿树种,具有重要的经济和药用价值。该研究以饭甑青冈叶片为材料,通过Illumina HiSeq X ten高通量测序平台,对其叶绿体基因组进行测序、组装和注释。结果表明,饭甑青冈叶绿体全基因组具有典型的四分体结构,全长为160796 bp,共注释129个基因,其中包括83个蛋白编码基因、38个tRNA基因和8个rRNA基因。密码子偏好性分析表明饭甑青冈的密码子使用模式偏向以A或U结尾,亮氨酸(Leu)密码子使用频率最高,半胱氨酸(Cys)使用率最低。重复序列分析共检测到292个SSR位点,其中单碱基重复的SSR位点最多,有183个,无六碱基重复。壳斗科叶绿体基因组比较分析显示,反向重复区的位置和边界区域的基因分布无明显的收缩与扩张现象。系统发育分析表明,饭甑青冈与云山青冈(C.sessilifolia)、小叶青冈(C.myrsinifolia)亲缘关系密切。该研究为饭甑青冈的分子标记、物种鉴定、遗传多样性分析等研究提供了基础。展开更多
基金supported by the National Natural Science Foundation of China(No.31901217)the Special Fund for Scientific Research of Shanghai Landscaping and City Appearance Administrative Bureau(grant numbers G192422,G242414,and G242416).
文摘Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hemisphere forests,and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations.Here we used a newly sequenced genome of Quercus gilva,an evergreen oak species from East Asia,with 18 published Fagales genomes to determine how Fagaceae genomes have evolved,identify genomic footprints of ecological adaptability in oaks in general,as well as between evergreen and deciduous oaks.We found that oak species exhibited a higher degree of genomic conservation and stability,as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events.In addition,we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense(e.g.,cuticle biosynthesis and oxidosqualene cyclase genes),which may represent the foundation for the ecological adaptation of oak species.Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks.This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic,genome evolutionary,and functional genomic analyses.
