黄背草与2种菅属植物叶绿体基因组特征比较及系统发育分析

目的 以黄背草Themeda japonica为试验材料，比较分析其与阿拉伯黄背草T. triandra、中华菅T. quadrivalvis2种同属植物的叶绿体基因组特征及其与近缘物种的系统发育关系。方法 采用Illumina HiSeq高通量测序平台首次对黄背草叶绿体基因组进行测序，使用SPAdes和CpGAVAS2分别对其进行组装和注释，并用Codon W、DnaSP和MISA等对其与2种同属植物进行一系列比较基因组分析，利用最大似然法（maximum likelihood,ML）构建系统进化树。结果 3个叶绿体基因组全长为138 735～138 961 bp，具有典型的四分体结构，共注释出129个基因；黄背草与其同属的2个物种相比，反向重复区（inverted repeats,IR）收缩了2132 bp，大单拷贝区（large single copy region,LSC）扩张了约4000 bp，而小单拷贝区（small single copy region,SSC）变化不大。密码子偏好性分析显示，3个叶绿体基因组相对丰度最大和最小的密码子都相同，同义密码子相对使用丰度略有不同...

Comparison of chloroplast genome characteristics and phylogenetic analysis between Themeda japonica and two species of Themeda

Objective Themeda japonica was used as the experimental material to compare its chloroplast genome characteristics with those of two congeners, T. triandra and T. quadrivalvis, and their phylogenetic relationships with the closely related species. Methods Using the Illumina HiSeq high throughput sequencing platform, the chloroplast genome of T. japonica was sequenced for the first time. SPAdes and CpGAVAS2 were used to assemble and annotate it, respectively. CodonW, DnaSP, and MISA were used to perform a series of comparative genomic analysis with two species of plants of the same genus, and the maximum likelihood (ML) method was used to construct a phylogenetic tree. Results The three chloroplast genomes were 138 735—138 961 bp in length, with a typical tetrad structure, and a total of 129 genes were annotated; compared with the two species of the same genus, the inverted repeats (IR) contracted by 2 132 bp, the large single copy region (LSC) expanded by about 4 000 bp, and the small single copy region (SSC) did not change much. Codon preference analysis showed that the codons with the highest and lowest relative abundance in the three chloroplast genomes were the same, while the relative abundance of synonymous codons was slightly different, but the difference was not significant. Nucleic acid polymorphism analysis showed that the nucleic acid polymorphism values (Pi) of the sequences in the inter-region of the three chloroplast genomes were generally higher than those of the shared gene sequences, and the IR region was more conserved than the LSC and SSC regions. A total of 38, 36 and 37 simple sequence repeats (SSR) and two long sequence repeats were detected in the three chloroplast genomes, respectively. Phylogenetic analysis indicated that T. japonica was most closely related to T. triandra. Conclusion The comparative analysis of chloroplast genome characteristics and phylogeny between T. japonica and two species of Themeda was carried out, laying the foundation for the species identification of the three species and the study of genetic diversity and phylogeny of Themeda.