鹅耳枥属树种叶绿体基因组结构及变异分析  

Structure and variation analyses of chloroplast genomes in Carpinus

作　　者：赵儒楠 褚晓洁 刘维 何倩倩 祝遵凌[1,3] ZHAO Runan;CHU Xiaojie;LIU Wei;HE Qianqian;ZHU Zunling(Co-Innovation Center for the Sustainable Forestry in Southern China,College of Landscape Architecture,Nanjing Forestry University,Nanjing 210037,China;College of Chemistry and Life Sciences,Zhejiang Normal University,Jinhua 321004,China;College of Art and Design,Nanjing Forestry University,Nanjing 210037,China)

机构地区：[1]南京林业大学风景园林学院,南方现代林业协同创新中心,江苏南京210037 [2]浙江师范大学化学与生命科学学院,浙江金华321004 [3]南京林业大学艺术设计学院,江苏南京210037

出　　处：《南京林业大学学报（自然科学版）》2021年第2期25-34,共10页Journal of Nanjing Forestry University：Natural Sciences Edition

基　　金：林业科技成果国家级推广项目(2019133119);江苏省“333工程”项目(BRA2018065);国家自然科学基金项目(31770752)。

摘　　要：【目的】了解鹅耳枥属(Carpinus)树种叶绿体基因组基因组成及结构特征,为鹅耳枥属的系统发育及基因组进化研究提供参考。【方法】获取鹅耳枥属16个树种的叶绿体基因组,对其进行基因注释,利用生物信息学方法比较叶绿体基因组间的结构特征与变异程度,并以麻栎(Quercus acutissima)为外类群分析了鹅耳枥属的系统发育关系。【结果】鹅耳枥属16个树种的叶绿体基因组均为双链环形结构,均包含1个长单拷贝区(LSC)、1个短单拷贝区(SSC)以及2个反向重复区(IRa和IRb)。叶绿体基因组大小差异较小,最大差异仅1 902 bp。基因排列顺序基本一致,各基因数量相对保守,其中核糖体RNA(rRNA)数量最为保守,所有树种均为8个。此外,鹅耳枥属树种叶绿体基因组在序列长度、基因组成以及GC含量等方面相对保守,但4个边界存在明显的多样性。鹅耳枥属叶绿体基因组中非基因编码区存在较大差异,变异程度较高,而基因编码区差异较小,具有较高的保守性。在叶绿体基因组4个部分中,LSC区的变异程度最高,IRa区的变异程度最低。鹅耳枥属叶绿体基因组中psbA、rps16、atpA、rps19、ndhF、ndhI以及ycf1等基因的编码区存在显著差异。此外,ycf3-trnS,trnS-rps4,trnH-psbA,psbZ-trnfM,matK-rps16,rps16-trnQ,trnQ-psbK,ccsA-ndhD,accD-psaI,ndhC-trnV,trnT-trnL,trnF-ndhJ,atpB-rbcL,trnT-psbD,trnE-trnT,trnD-trnY,rpl32-trnl等基因间隔区的非编码区差异较大。绝大部分基因的编码区长度十分保守,含内含子的蛋白编码基因长度变异主要来源于内含子长度或编码区长度。系统发育分析结果将鹅耳枥属划分为鹅耳枥组与千金榆组,此外由于地理隔离导致欧洲鹅耳枥(C.betulus)、美洲鹅耳枥(C.caroliniana)与鹅耳枥属其他树种表现出较远的亲缘关系。【结论】鹅耳枥属树种叶绿体基因组具有较高的保守性,其基因排列顺序基本一致,未检测到大规模的倒位或�【Objective】Chloroplasts are the organelles responsible for the photosynthesis in green plants. The chloroplast genome structure and gene composition of higher plants are relatively conservative, but can show different degrees of variation due to hybridization, evolution and gene introgression. It contains a significant amount of DNA information, which is used in species classification, phylogeny and origin. Carpinus is one of the most evolved genus in the Betulaceae family. Although the chloroplast genomes of more than ten species of Carpinus have been sequenced and assembled, only a few of these have been fully studied. Therefore, this study aimed to understand the chloroplast genome gene composition and structural characteristics of Carpinus, reveal the contraction and expansion of the inverted repeat(IR) region boundary, and lay a foundation for further studies on phylogenetic relationships, species identification, genome evolution and resource utilization and provide a reference for the development of Carpinus DNA barcoding. 【Method】GeSeq was used to annotate the chloroplast genome with Ostrya rehdariana as the reference genome. Then, the number of genes, genomic DNA base composition(GC) content, large single copy(LSC), small single copy(SSC) and two IR regions of the chloroplast genomes of 16 Carpinus species were obtained. The structure, boundary contraction and expansion, and sequence variation were then compared by using OGDRAW, IRscope and mVISTA programs. The phylogenetic relationship of Carpinus was analyzed with Quercus acutissima as an outgroup. 【Result】We found that the chloroplast genomes of 16 species were circular, double-stranded, which were tetrads containing one LSC and SSC and two IRs. The difference in genome size was small, and the maximum difference was only 1 902 bp. The differences in IR region length and GC content among species were small. The gene sequence length and composition were relatively conservative, with the number of rRNAs(8) as the most conservative;however, the

关 键 词：鹅耳枥属 叶绿体基因组 变异 进化 系统发育 

分 类 号：Q941[生物学—植物学]