Chloroplast Genome Structure and Phylogenetic Relationships in the Alpine Endemic Plant Pleurospermum foetens
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摘要: 本文基于高通量技术对丽江棱子芹(Pleurospermum foetens)的叶绿体基因组进行测序，并对丽江棱子芹的叶绿体基因组结构特征及其系统进化关系进行了分析。结果表明，丽江棱子芹的叶绿体基因组具备典型的四分体结构，基因组全长155 057 bp,包含87个蛋白编码基因、 8个核糖体RNA基因和39个转运RNA基因。生物信息学分析结果显示，叶绿体基因组共编码26 075个密码子，编码异亮氨酸Ile的ATT数量最多，除终止子外编码半胱氨酸Cys的TGC数量最少，相对同义密码子使用度最高的为UUA,最少的是AGC; SSR位点共预测到了34个，包括单核苷酸重复序列27个，双核苷酸重复序列4个，以及复合型重复序列3个。丽江棱子芹与棱子芹属(Pleurospermum)其他植物相比较，其基因组大小、基因类型及GC含量相近。利用IQ-TREE软件构建最大似然树，结果表明丽江棱子芹与线裂棱子芹(P.linearilobum)的亲缘关系最近，棱子芹属为多系类群。该研究丰富了丽江棱子芹叶绿体基因组的遗传信息，为丽江棱子芹的分子标记的开发、遗传多样性和谱系地理研究等奠定了理论基础，同时也为构建伞形科(Apiaceae)植物的系统进化提供了支持。Abstract: This study sequenced the chloroplast genome of Pleurospermum foetens by high throughput technique, and analyzed its structural characteristics and phylogenetic relationship. The results showed that the chloroplast genome was a typical tetrad structure. The total length of the genome is 155 057 bp, with 87 protein coding genes, 8 ribosomal RNA genes, and 39 transfer RNA genes. Bioinformatics analysis revealed that the chloroplast genome encodes a total of 26 075 codons, with the highest number of ATT coding for Ile and the lowest number of TGC coding for Cys, apart from the terminator. The highest relative synonymous codon usage was UUA, and the lowest was AGC. Additionally, 34 SSR loci were identified, including 27 single nucleotide repeats sequences, 4 double nucleotide repeats sequences, and 3 complex repeats sequences. The genome size, gene type and GC content of P. foetens were similar with other Pleurospermum species. A maximum likelihood tree was constructed using the IQ-TREE software, the results showed that P.foetens is closely related to P.linearilobum and the Pleurospermum branch is a paraphyletic group. This study enriched the genetic information of chloroplast genome of P. foetens, and laid a theoretical foundation for the development of molecular markers, genetic diversity and phylogeography of P. foetens. It also provides support for the systematic evolution of Apiaceae plants.
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