卵叶远志叶绿体基因组序列特征与系统发育分析

目的 解析卵叶远志Polygala sibirica叶绿体因组的序列特征和系统发育关系。方法 利用CTAB法提取卵叶远志叶片基因组DNA,通过IlluminaHi Seq平台测序,再用Get Cellelle组装叶绿体基因组,通过MEGA11构建邻接法（neighbor-joining,NJ法）系统发育树。结果 卵叶远志的叶绿体基因组全长165192bp,GC含量为36.70%,共编码124个基因,其中包含8个rRNA基因、42个tRNA基因和74个蛋白编码基因;相对同义密码子使用度显示,67.29%的密码子的使用度>1,密码子偏好A、T结尾;共检测到287个简单重复序列（simple sequence repeats,SSR）,其中以单核苷酸重复次数最多,占80.61%,单核苷酸主要由A和T组成,这表明在碱基形成过程中A和T被频繁使用;边界分析显示,9种远志属植物叶绿体基因组边界较为稳定,卵叶远志、香港远志P. hongkongensis、远志P. tenuifolia、瓜子金P. japonica和合叶草P. subopposite基因结构存在相似性;变异分析显示,9种远志属...

Chloroplast genome sequence characteristics and phylogenetic analysis of Polygala sibirica

Objective To identify the sequence characteristics and phylogenetic relationships of Polygala sibirica chloroplast genome. Methods The genomic DNA of leaves was extracted by CTAB method and sequenced by the Illumina HiSeq platform, and the chloroplast genome was assembled by GetCellelle, and the neighbor-joining (NJ) phylogenetic tree was constructed by MEGA11. Results The total length of the chloroplast genome of P. sibirica was 165 192 bp, with a GC value of 36.70%. The chloroplast genome of P. sibirica has 124 coding genes, with the numbers of CDS, tRNA, and rRNA were 74, 42, and 8, respectively; relative synonymous codon usage showed that 67.29% of codons had a usage level large than 1, and codons preferred A and T endings. A total of 287 simple sequence repeats (SSRs) were detected, and the number of single nucleotide repetitions was the highest, accounting for 80.61 %. Mononucleotides are mainly composed of A and T, indicating that A and T are frequently used during base formation. Boundary analysis showed that the chloroplast genome boundaries of nine species of Polygala were relatively stable, and the gene structures of P. sibirica, P. hongkongensis, P. tenuifolia, P. japonica and P. subopposita were similar. Variation analysis showed that the chloroplast genome variation of nine species of Polygala was small. The results of phylogenetic analysis showed that P. sibirica, P. hongkongensis, P. japonica, P. tenuifolia, P. subopposite and P. crotalarioide could be clustered into one branch due to their high support rates. Conclusion The high-quality whole chloroplast genome of P. sibirica was constructed, which laid a foundation for the study of genetic structure and genetic diversity of P. sibirica.