锈毛钝果寄生叶绿体基因组的序列特征和系统发育分析

Chloroplast genome sequence characterization and phylogenetic analysis of Taxillus levinei

目的 以药用植物锈毛钝果寄生Taxilluslevinei为材料,在高通量测序、组装的基础上,明确叶绿体因组的结构、序列特征和系统发育关系。方法 利用SDS法提取基因组DNA,采用Illumina HiSeq X Ten进行高通量测序,用Novo Plasty组装叶绿体基因组,借助PhyML生成系统发育树。结果 锈毛钝果寄生的叶绿体基因组全长为122 208 bp,GC值为37.3%,大单拷贝区(large single copy region,LSC)、小单拷贝区(small single copy region,SSC)和反向重复区(inverted repeat region,IR)的长度分别为70 522、6084和22 801 bp;锈毛钝果寄生的叶绿体基因组共有基因108个,其中的编码蛋白基因、t RNA与r RNA分别为66、29和8个,另有5个假基因;inf A基因、所有的ndh基因及6个t RNA发生丢失。序列比对结果表明,锈毛钝果寄生与桑寄生T. sutchuenensis (Lecomte) Danser叶绿体基因组之间的相似性最高,达96.7%。系统发育分析结果表明,7种植物在发育树上分成5组,其中,锈毛钝果寄生与桑寄生和广寄生聚于一组。结论 锈毛钝果寄生叶绿体基因组的组装、序列分析和系统发育分析,为后续开展遗传结构和遗传多样性研究奠定了基础,并为桑寄生科植物的进化和系统发育研究提供了依据。

Objective In the present study,based on high-throughput sequencing and genome assembly methods,chloroplast genome structure,sequence characters,and phylogenetic relationships of Taxillus levinei were confirmed.Methods The SDS-based DNA extraction method was applied to prepare genomic DNA,and the Illumina HiSeq X Ten System was used for high-throughput sequencing.NovoPlasty was chosen to assemble chloroplast genome.A phylogenetic tree was generated using PhyML.Results The complete chloroplast genome of T.levinei was 122208 bp in length with a GC content of 37.3%,and the sizes of LSC,SSC,and IR were 70522 bp,6084 bp,and 22801 bp,respectively.The chloroplast genome harbored 108 genes,and the numbers of protein-coding genes,tRNAs,and rRNAs were 66,29 and 8,respectively.Additionally,there existed five pseudogenes.Genes including infA,all ndhs,and six tRNAs were completely lost.Sequence comparison results indicated that the highest similarity was observed between T.levinei and T.sutchuenensis,which reached 96.7%.Phylogenetic analysis revealed that the seven plants could be divided into five groups,and among them,T.levinei and T.sutchuenensis were found to be gathered in the same clade,showing their highest sequence similarity.Conclusion The assembly,sequence analysis,and phylogenetic analysis of T.levinei chloroplast genome provide insight into further studies on genetic structure and genetic diversity,and the results also provide evidences for evolution and phylogenetic analysis of Loranthaceae plants.