中国特有苏铁属植物叶绿体比较基因组学研究  

Comparative Study on Chloroplast Genomics of Cycas Plants Endemic to China

作　　者：余潇[1] 宋雨茹 赵振宁 刘子榕 YU Xiao;SONG Yu-ru;ZHAO Zhen-ning;LIU Zi-rong(College of Landscape Architecture and Horticulture,Southwest Forestry University,Kunming 650224,China;College of Forestry,Southwest Forestry University,Kunming 650224,China)

机构地区：[1]西南林业大学园林园艺学院,昆明650224 [2]西南林业大学林学院,昆明650224

出　　处：《沈阳农业大学学报》2023年第1期53-65,共13页Journal of Shenyang Agricultural University

基　　金：云南省第二次国家重点保护野生植物资源调查项目(09930-216304);2021年度云南省大学生创新创业国家级项目(202110677046)。

摘　　要：为了解中国特有9种苏铁属(Cycas)植物叶绿体基因组及结构特征,为苏铁属的系统发育及基因组进化研究提供参考。获取苏铁属9个物种的叶绿体基因组,利用生物信息学方法比较叶绿体基因组之间结构特征和与变异程度。结果表明:所有苏铁属植物叶绿体基因组均为双链环状结构,叶绿体基因组大小为161 993~163 403 bp,叶绿体基因组大小差异较小。9种苏铁属植物的叶绿体基因组各基因数量相对保守,总基因数为131~135个,蛋白质编码基因为87或89个,rRNA数量最为保守,均为8个。叶绿体基因组均含有46~54个SSR位点,主要以单核苷酸和四核苷酸为主,未检测出五核苷酸和六核苷酸。苏铁属植物之间离散重复序列差异较大,重复序列总数介于50~288之间,所有物种的长度均集中分布于30~39 bp这个区间范围内。苏铁属植物叶绿体基因组边界扩张收缩较为稳定相似,只在个别种中发生了较小的变异。苏铁属9种植物的非编码区变异大于编码区,同时大单拷贝区(LSC)的变异程度最高,而反向重复区(IRa)的变异程度最低。苏铁属叶绿体基因组中ycf12、atpH、psbM、ndhG和chlL等基因编码区存在显著差异,同时trnK-UUU、trnF-GAA、trnC-GCA、trnM-CAU、trnH-GUG、trnL-CAA、trnP-GGG、trnH-GUG等基因间隔区的非编码区也存在不同程度的变异,这些基因可以作为苏铁属植物分子鉴定的候选基因。9种苏铁属植物的同义密码子以A和U结尾,是该属叶绿体基因组偏好的密码子;其共有最优密码子有12个,分别为GCU、CGU、CAA、GGU、AUC、CUA、CCU、UCU、ACC、ACU、GUA、GUU。基于叶绿体全基因组和CDS序列构建的系统发育关系既具有一定的相似性,也存在一些差异。研究结果对苏铁属植物的系统发育研究和分子标记开发等提供了参考依据。To understand the chloroplast genome and structural characteristics of nine species of Cycas endemic to China,and to provide references for the phylogeny and genome evolution of Cycas.The chloroplast genomes of nine Cycas species were obtained,and the structural characteristics and variation degree of the chloroplast genomes were compared using bioinformatics methods.The results showed that the chloroplast genome of Cycas had a double-stranded circular structure,and the genome size ranged from 161 993to 163 403 bp.The number of genes in the chloroplast genomes of nine Cycas species was relatively conserved.The total number of genes varied from 131 to 135,the number of protein-coding genes was 87 or 89,and the number of rRNA genes was most conserved at 8.The chloroplast genome contained 46-54 SSR sites,mainly mononucleotides and tetranucleotides,and pentanucleotides and hexanucleotides were not detected.The total number of repeats ranged from 50 to 288,and the length of all species was concentrated between 30 to 39 bp.The boundary expansion and contraction of the Cycas chloroplast genome is relatively stable and similar,with only minor changes occurring in some species.The variation of non-coding region of 9 Cycas was greater than that of coding region,among which the variation of large single-copy region(LSC) was the largest,and that of inverted repeat region(IRa) was the lowest.There were significant differences in the coding regions of ycf12,atpH,psbM,ndhG and chlL genes in the chloroplast genome of Cycas,and the non-coding regions of trnK-UUU,trnF-GAA,trnC-GCA,trnM-CAU,trnH-GUG,trnL-CAA,trnP-GGG and trnH-GUG also had different degrees of variation.These genes can be used as candidate genes for molecular identification of Cycas.The synonymous codons of the nine Cycas plants end with A and U,which are the preferred codons of the chloroplast genome of the genus;there are12 optimal codons,GCU,CGU,CAA,GGU,AUC,CUA,CCU,UCU,ACC,ACU,GUA and GUU.The phylogenetic relationship based on chloroplast genome and CDS sequence

关 键 词：苏铁属 叶绿体基因组 重复序列 序列变异 系统发育分析 

分 类 号：Q754[生物学—分子生物学] Q789