| 摘要: |
| 为了研究广藿香（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、多态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及15~18个回文重复序列、12~17个正向重复序列。（6）经遗传距离分析与系统发育分析，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基础资料。 |
| 关键词: 广藿香 叶绿体基因组 重复序列 多态性 同义密码子相对使用度 |
| DOI：10.11931/guihaia.gxzw202402031 |
| 分类号: |
| Fund project: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 of 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
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| Abstract: |
| Pogostemon cablin (Blanco) Benth. 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 environment 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 through the OGDRAW website, and analyzed the basic structural characteristics, IR/SC boundary comparison, genome comparison and collinearity analysis, simple repeat sequences and interspersed repeat sequences, polymorphism 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 patchouli was 152 461~152 510 bp, and 132 genes were annotated, including 87 CDS, 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)Analysis of the relative usage of synonymous codons detected a total of 64 codons encoding 20 amino acids, and there were 33 highly preferred codons, among which codons ending in A/U accounted for the majority. (5)74-76 SSRs, 15-18 palindrome repeat sequences, and 12-17 forward repeat sequences were detected. (6)After genetic distance analysis and phylogenetic analysis, only GSY_MLXY has a distant genetic relationship with other cultivated types. In this study, the genome structure and different sites identified of chloroplasts from 20 different sources of P. cablin were obtained, which provided basic data for the development of molecular markers and the selection of superior germplasm. |
| Key words: Pogostemon cablin (Blanco) Benth. chloroplast genome repetitive sequence single nucleotide polymorphism relative usage of synonymous codon |
