资源植物黑老虎的比较叶绿体基因组学研究

翟学昌; 彭丽; 颜海飞; 朱柯帆; 张淑燕; 张彩云; 鲁显楷

doi:10.12302/j.issn.1000-2006.202404014

资源植物黑老虎的比较叶绿体基因组学研究

翟学昌, 彭丽, 颜海飞, 朱柯帆, 张淑燕, 张彩云, 鲁显楷

南京林业大学学报（自然科学版） ›› 2024, Vol. 48 ›› Issue (6) : 71-78.

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南京林业大学学报（自然科学版） ›› 2024, Vol. 48 ›› Issue (6) : 71-78. DOI: 10.12302/j.issn.1000-2006.202404014

研究论文

资源植物黑老虎的比较叶绿体基因组学研究

翟学昌 ¹ ,
彭丽 ¹ ,
颜海飞 ²^,^* ,
朱柯帆 ³ ,
张淑燕 ²^,⁴ ,
张彩云 ⁵ ,
鲁显楷 ²

作者信息 +

Comparative chloroplast genomics of the important resource plant Kadsura coccinea

ZHAI Xuechang ¹ ,
PENG Li ¹ ,
YAN Haifei ²^,^* ,
ZHU Kefan ³ ,
ZHANG Shuyan ²^,⁴ ,
ZHANG Caiyun ⁵ ,
LU Xiankai ²

Author information +

文章历史 +

摘要

【目的】发掘我国重要资源植物黑老虎(Kadsura coccinea)的叶绿体基因组高变异区域及SSR变异位点,为其遗传多样性及种质资源评估奠定基础。【方法】获取5个黑老虎个体的叶绿体基因组,通过基因注释,采用生物信息学方法开展核苷酸多态性、简单重复序列(simple sequarce repeat,SSR)分析,并以2个五味子属植物为外类群分析南五味子属的系统发育关系。【结果】黑老虎完整叶绿体基因组为典型的四分体环状结构,长度为145 413~145 903 bp。其中,大单拷贝区的长度范围为94 457~94 757 bp,小单拷贝区的长度为18 032~18 047 bp,重复区为16 431~16 552 bp。黑老虎叶绿体基因组编码125个基因,蛋白编码基因、tRNA基因、rRNA基因分别为82、35、8个;总G(鸟嘌呤)和C(胞嘧啶)的碱基数占总碱基数的比例(GC占比)为39.7%。采用滑动窗口法分析发现黑老虎叶绿体基因组上petN-psbM和trnS-GCU-trnG-UCC具有很高的核苷酸多态性(P_i > 0.03)。该物种叶绿体基因组上共有212个SSR位点,其中24个SSR位点在5个黑老虎个体间存在多态变异,具有应用前景。系统发育分析表明,此次研究中黑老虎个体聚成一支,与同属其他物种关系较远。【结论】本研究首次系统比较了多个黑老虎个体的叶绿体基因组,发掘出基因组内的高变异区域及变异SSR位点,为其遗传多样性及种质资源评估奠定了基础。

Abstract

【Objective】This study aims to investigate the chloroplast genomes and SSR loci of Kadsura coccinea, an important plant resource in China, to establish a basis for assessing its genetic diversity and germplasm resources.【Method】The study obtained and analyzed the chloroplast genomes of five individuals of K. coccinea through genetical annotation, nucleotide polymorphism analysis, and SSR analysis using bioinformatics methods. Additionally, the phylogenetic analysis of Kadsura were reconstructed using two Schisandra spp. as outgroups.【Result】The chloroplast genome of K. coccinea showed a typical quadripartite structure, with genome lengths ranging from 145 413 to 145 903 base pairs (bp). The large single-copy region (LSC) spaned from 94 457 to 94 757 bp, while the small single-copy region (SSC) encompassed 18 032 to 18 047 bp. It encodes a total of 125 genes, including 82 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The genome had a total GC content of 39.7% and demonstrated substantial nucleotide polymorphisms (P_i > 0.03) in the intergenic regions of petN-psbM and trnS-GCU-trnG-UCC. A total of 212 single sequence repeat (SSR) loci were identified across the chloroplast genomes of this species. Mononucleotide repeats were the most prevalent, followed by trinucleotide repeats, and pentanucleotide repeats were the least frequent. Among these loci, 24 polymorphic SSR loci were found among five individuals of K. coccinea, indicating their potential utility in future. Phylogenetic analysis robustly clusters K. coccinea individuals into a distinct group, revealing no close relationship with other congeneric species.【Conclusion】This study presents the first systematic comparison of chloroplast genomes among multiple K. coccinea individuals. Our findings identified highly variable regions and SSR loci that can be valuable for evaluating the genetic diversity and germplasm resource of this species.

导出引用

翟学昌, 彭丽, 颜海飞, 等. 资源植物黑老虎的比较叶绿体基因组学研究[J]. 南京林业大学学报（自然科学版）. 2024, 48(6): 71-78 https://doi.org/10.12302/j.issn.1000-2006.202404014

ZHAI Xuechang, PENG Li, YAN Haifei, et al. Comparative chloroplast genomics of the important resource plant Kadsura coccinea[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2024, 48(6): 71-78 https://doi.org/10.12302/j.issn.1000-2006.202404014

中图分类号： S718;Q754

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