连香树叶绿体基因组测序与特征分析

Genome Sequencing and Characteristic Analysis of Cercidiphyllum japonicum

为明确连香树叶绿体基因组的大小、结构、基因组成、简单重复序列(SSR)位点、密码子偏好性及近缘种的关系,本研究以连香树为原材料,提取其基因组DNA,建立测序文库,然后进行测序、组装、SSR分析、密码子偏好性分析及系统发育分析。结果显示,连香树叶绿体基因组全长为159 854 bp,总GC含量为37.9%,具有叶绿体典型的四分体结构,包括大单拷贝区(LSC) 88 035 bp,小单拷贝区(SSC) 18 965 bp,反向重复序列(IR) 26 427 bp。经注释共编码134个基因,其中编码蛋白质的基因90个、编码rRNA的基因8个以及编码tRNA的基因36个。经序列分析共鉴定出52个SSR位点,其中单核苷酸重复为43个,二核苷酸重复为7个,三核苷酸重复为1个,四核苷酸重复为1个,所有的重复基元均为A/T碱基。连香树叶绿体基因组的有效密码子数(ENc)为55.05,说明其密码子偏好性较弱。其密码子的GC含量(38.9%)和密码子第3位的GC含量(35.4%)均低于50%,同义密码子相对使用度(RSCU)高于1的密码子共有33个,其中以A或U碱基结尾占87.88%,说明连香树叶绿体基因组的密码子偏向以A或U碱基结尾。系统发育分析显示,连香树与金缕梅亲缘关系最近,表明两者在进化上具有共线性。本研究检测了连香树完整叶绿体基因组,并对其进行特征分析,为进一步研究提供基本遗传资源。

In order to clarify the size,structure,gene composition,SSR loci,codon preference,and the relationship with related species,C.japonicum was used as the raw material,its genomic DNA was extracted,a sequencing library was established,then sequencing,assembly,SSR analysis,codon preference and phylogeny analysis were performed.The results showed that the total length of the chloroplast genome of C.japonicum was 159 854 bp,and the total GC content was 37.9%.It had a typical chloroplast tetrad structure,including the LSC of 88 035 bp,the SSC of 18 965 bp,and the IR of 26 427 bp.A total of 134 genes were annotated,including 90 protein-coding genes,8 rRNA genes and 36 t RNA genes.A total of 52 SSR loci were identified through sequence analysis,including 43 mononucleotide repeats,7 dinucleotide repeats,1 trinucleotide repeats and 1 tetranucleotide repeats.All repetitive motifs were A/T bases.The ENc value of the chloroplast genome was 55.05,indicating that its codon preference was weak.The GC content of the codons in the chloroplast genome was 38.9%,and the GC content of the third position of the codon was 35.4%,both of which were lower than 50%.In addition,there were 33 codons with RSCU value higher than 1,of which 87.88% end with A or U bases,which indicates that the codons of the chloroplast genome tend to end with A or U bases.Phylogenetic analysis showed that the relationship between C.japonicum and Hamamelis mollis was the closest,indicating that the two were evolutionarily co-linear.In this study,the complete chloroplast genome of C.japonicum was detected,and its characteristics were analyzed to provide basic genetic resources for further research.