| 引用本文: | 行冰楠, 梁莹莹, 吴文如, 陆亚茹, 邹何元, 彭晓祺.不同来源广藿香叶绿体基因组研究[J].广西植物,2025,45(4):716-729.[点击复制] |
| XING Bingnan, LIANG Yingying, WU Wenru, LU Yaru, ZOU Heyuan, PENG Xiaoqi.Analysis of chloroplast genome of Pogostemon cablin from different origins[J].Guihaia,2025,45(4):716-729.[点击复制] |
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| 不同来源广藿香叶绿体基因组研究 |
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行冰楠, 梁莹莹, 吴文如*, 陆亚茹, 邹何元, 彭晓祺
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广州中医药大学 中药学院, 广州 510006
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| 摘要: |
| 为探究广藿香(Pogostemon cablin)叶绿体基因组的结构特征,比较不同来源广藿香叶绿体基因组的差异,该研究利用DNBSeq测序平台对广藿香全基因组进行测序,使用GetOrganelle组装完整的广藿香叶绿体基因组,通过CPGAVAS2网站对该叶绿体基因组进行注释,对不同来源的广藿香叶绿体基因组进行基本结构特征分析、IR/SC的边界比较、基因组比较及共线性分析、简单重复序列及散在重复序列、多样性分析和同义密码子相对使用度分析。结果表明:(1)20个不同来源广藿香叶绿体基因组全长为152 461～152 510 bp,注释得到132个基因,其中包含87个CDS、37个tRNA基因和8个rRNA基因。(2)mVISTA比对发现atpF、atpF-atpH、rps16-trnQ-UUG、rpoB-trnC-GCA、accD、psaI-ycf4、petA-psbJ、rpl16、rps15-ycf1为高变区。(3)核酸多样性大于0.002的位点位于trnM-CAU-atpB间隔区、ycf4、rpl32、rpl32-trnL-UAC间隔区。(4)检测到共有64种密码子编码20个氨基酸,偏好性较强的密码子有33个,其中以A/U结尾的密码子占大多数。(5)检测出74～76个SSR、15～18个回文重复序列及12～17个正向重复序列。(6)遗传距离分析与系统发育分析发现,仅GSY_MLXY与其他栽培类型的亲缘关系较远。该研究获得了20个不同来源广藿香叶绿体基因组结构信息以及差异位点,为分子标记的开发及优良种质筛选提供了基础资料。 |
| 关键词: 广藿香, 叶绿体基因组, 重复序列, 多样性, 同义密码子相对使用度 |
| DOI：10.11931/guihaia.gxzw202402031 |
| 分类号:Q943.2 |
| 文章编号:1000-3142(2025)04-0716-14 |
| 基金项目:中央本级重大增减支项目“名贵中药资源可持续利用能力建设项目”(2060302); 广州中医药大学大学生创新创业训练计划项目(202210572232)。 |
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| Analysis of chloroplast genome of Pogostemon cablin from different origins |
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XING Bingnan, LIANG Yingying, WU Wenru*, LU Yaru, ZOU Heyuan, PENG Xiaoqi
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School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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| Abstract: |
| Pogostemon cablin possesses significant medical and industrial values, as it can be used for medicinal purposes as well as for essential oil extraction. However, the yield and quality of P. cablin can vary depending on the ecological environments and artificial cultivation measures employed in different production regions and origins. In order to study the structural characteristics and compare the differences of the chloroplast genome of P. cablin of different origins, this study used the DNBSeq sequencing platform to sequence the whole genome of P. cablin, used GetOrganelle to assemble the complete chloroplast genome, annotated the chloroplast genome on the CPGAVAS2 website, and analyzed the basic structural characteristics, IR/SC boundary comparison, genome comparison and collinearity analysis, simple repeat sequences and interspersed repeat sequences, diversity analysis and relative usage analysis of synonymous codons. The results were as follows:(1)The full length of the chloroplast genomes of 20 different origins of P. cablin was 152 461-152 510 bp, and 132 genes were annotated, including 87 CDSs, 37 tRNA genes and 8 rRNA genes.(2)The mVISTA comparison found that atpF, atpF-atpH, rps16-trnQ-UUG, rpoB-trnC-GCA, accD, psaI-ycf4, petA-psbJ, rpl16, and rps15-ycf1 were hypervariable regions.(3)The sites with nucleic acid diversity greater than 0.002 were located in the trnM-CAU-atpB interval, ycf4, rpl32, and rpl32-trnL-UAC interval.(4)A total of 64 codons encoding 20 amino acids were detected, and there were 33 highly preferred codons, among which codons ending in A/U accounted for the majority.(5)And 74-76 SSRs, 15-18 palindrome repeat sequences, and 12-17 forward repeat sequences were detected.(6)Genetic distance analysis and phylogenetic analysis found that only GSY_MLXY had a distant genetic relationship with other cultivated types. In this study, the genome structure information and different sites identified of chloroplasts from 20 different sources of P. cablin are obtained, which provides basic data for the development of molecular markers and the selection of superior germplasm. |
| Key words: Pogostemon cablin, chloroplast genome, repetitive sequence, diversity, relative synonymous codon usage |
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