Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae)
<i>Pogostemon</i> Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-11-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/9/11/1497 |
| _version_ | 1827702732627116032 |
|---|---|
| author | Cai-Yun Zhang Tong-Jian Liu Xiao-Lu Mo Hui-Run Huang Gang Yao Jian-Rong Li Xue-Jun Ge Hai-Fei Yan |
| author_facet | Cai-Yun Zhang Tong-Jian Liu Xiao-Lu Mo Hui-Run Huang Gang Yao Jian-Rong Li Xue-Jun Ge Hai-Fei Yan |
| author_sort | Cai-Yun Zhang |
| collection | DOAJ |
| description | <i>Pogostemon</i> Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of <i>Pogostemon</i>, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., <i>Pogostemon plectranthoides</i> Desf., <i>P. septentrionalis</i> C. Y. Wu et Y. C. Huang, and two cultivars of <i>P. cablin</i> (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of <i>P. yatabeanus</i> (Makino) Press and <i>P. stellatus</i> (Lour.) Kuntze) suggested that <i>Pogostemon</i> cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (<i>Pi</i>) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and <i>Pogostemon.</i> For the overall mean substitution rates, the synonymous (<i>d</i><sub>S</sub>) and nonsynonymous (<i>d</i><sub>N</sub>) substitution rate values of protein-coding genes varied approximately threefold, while the <i>d</i><sub>N</sub> values among different functional gene groups showed a wider variation range. Overall, the cp genomes of <i>Pogostemon</i> will be useful for phylogenetic reconstruction, species delimitation and identification in the future. |
| first_indexed | 2024-03-10T15:03:42Z |
| format | Article |
| id | doaj.art-024363eef0ff411184903d66c055ce20 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T15:03:42Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-024363eef0ff411184903d66c055ce202023-11-20T19:55:39ZengMDPI AGPlants2223-77472020-11-01911149710.3390/plants9111497Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae)Cai-Yun Zhang0Tong-Jian Liu1Xiao-Lu Mo2Hui-Run Huang3Gang Yao4Jian-Rong Li5Xue-Jun Ge6Hai-Fei Yan7Guangdong Food and Drug Vocational College, Guangzhou 510520, ChinaKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaGuangdong Food and Drug Vocational College, Guangzhou 510520, ChinaKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaSouth China Limestone Plants Research Centre, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China<i>Pogostemon</i> Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of <i>Pogostemon</i>, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., <i>Pogostemon plectranthoides</i> Desf., <i>P. septentrionalis</i> C. Y. Wu et Y. C. Huang, and two cultivars of <i>P. cablin</i> (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of <i>P. yatabeanus</i> (Makino) Press and <i>P. stellatus</i> (Lour.) Kuntze) suggested that <i>Pogostemon</i> cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (<i>Pi</i>) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and <i>Pogostemon.</i> For the overall mean substitution rates, the synonymous (<i>d</i><sub>S</sub>) and nonsynonymous (<i>d</i><sub>N</sub>) substitution rate values of protein-coding genes varied approximately threefold, while the <i>d</i><sub>N</sub> values among different functional gene groups showed a wider variation range. Overall, the cp genomes of <i>Pogostemon</i> will be useful for phylogenetic reconstruction, species delimitation and identification in the future.https://www.mdpi.com/2223-7747/9/11/1497Pogostemoneaenucleotide diversityphylogenygenome skimming |
| spellingShingle | Cai-Yun Zhang Tong-Jian Liu Xiao-Lu Mo Hui-Run Huang Gang Yao Jian-Rong Li Xue-Jun Ge Hai-Fei Yan Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) Plants Pogostemoneae nucleotide diversity phylogeny genome skimming |
| title | Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) |
| title_full | Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) |
| title_fullStr | Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) |
| title_full_unstemmed | Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) |
| title_short | Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in <i>Pogostemon</i> (Lamiaceae) |
| title_sort | comparative analyses of the chloroplast genomes of patchouli plants and their relatives in i pogostemon i lamiaceae |
| topic | Pogostemoneae nucleotide diversity phylogeny genome skimming |
| url | https://www.mdpi.com/2223-7747/9/11/1497 |
| work_keys_str_mv | AT caiyunzhang comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT tongjianliu comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT xiaolumo comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT huirunhuang comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT gangyao comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT jianrongli comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT xuejunge comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae AT haifeiyan comparativeanalysesofthechloroplastgenomesofpatchouliplantsandtheirrelativesinipogostemonilamiaceae |