毛叶樟叶绿体全基因组序列特征与系统发育

Genomic Sequence Characteristics and Phylogeny of Chloroplast in Cinnamomum mollifolium

毛叶樟为樟科樟属常绿阔叶芳香树种,为了解其叶绿体基因组结构及系统发育,本研究利用高通量测序技术,绘制了毛叶樟叶绿体基因组物理图谱,分析了基因组序列特征。毛叶樟叶绿体基因组全长为152763 bp,GC含量为39.16%,具有一个大单拷贝区(large single-copy,LSC)、一个小单拷贝区(small single-copy,SSC)和两个反向重复区(inverted repeats,IRs),大小分别为93684、18931和20074 bp,共注释得到125个基因,包括36个tRNA基因,8个rRNA基因和81个蛋白编码基因,密码子偏向使用A/T碱基。MISA分析共检测出122个SSRs位点,富含A-T重复。核酸多态性分析结果显示3种樟属植物间的变异度较小,5种樟科植物的变异度较大,其SSC区域为高变区(Pi>0.2),包括ycf1、ccsA、psaC、rpl32和一系列ndh基因的蛋白编码区。系统分析结果支持毛叶樟为樟组植物,与细毛樟、云南樟聚为一小枝,亲缘关系更近。本研究为毛叶樟保护工作提供重要的遗传背景信息,也为樟属植物的系统进化及分类鉴定研究提供科学依据。

Cinnamomum mollifolium is an evergreen broad-leaved aromatic tree species of the Cinnamomum genus in Lauraceae family.In order to understand its chloroplast genome structure and phylogeny,we reported the complete sequencing of the chloroplast genome of C.mollifolium using illumina technology.The chloroplast genome of C.mollifolium is 152 763 bp in length,the GC content is 39.16%,and characterized by a relatively conserved quadripartite structure containing a large single-copy(LSC) region of 93 684 bp,a small single-copy(SSC) region of 18 931 bp and two inverted repeats(IRs) regions of 20 074 bp.A total of 125 genes were annotated that include 36 tRNA genes,8 rRNA genes and 81 protein-coding genes,of which 12 were repeated in the IR regions.The 122 SSRs,rich in A-T repeats,were detected by MISA.The C.mollifolium chloroplast genome showed weak codon preference,and the codons were biased to use A and T bases.An analysis of chloroplast sequence divergence revealed that the differences between the three Cinnamomum genomes were small,but the entir e SSC regions were highly variable(Pi>0.2) among the different genera in the Lauraceae family,including those of ycf1,psaC,ccsA,rpl32 and a set of genes named ndh coding regions.A phylogenetic analysis indicated that C.mollifolium is most closely related to Cinnamomum tenuipile and Cinnamomum glanduliferum.The complete sequence of the chloroplast of C.mollifolium will aid in in-depth taxonomical and development of specific DNA fingerprints studies of the Cinnamomum in the future and provides important genetic background information for the protection of C.mollifolium.