Plant Diversity ›› 2021, Vol. 43 ›› Issue (01): 15-26.DOI: 10.1016/j.pld.2020.07.004
Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)
Hong Wua,b, Peng-Fei Maa, Hong-Tao Lia, Guo-Xiong Huc, De-Zhu Lia
- a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b University of Chinese Academy of Sciences, Beijing, 100049, China;
c College of Life Sciences, Guizhou University, Guiyang, Guizhou, 550025, China
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收稿日期:2020-02-05修回日期:2020-07-13出版日期:2021-02-25发布日期:2021-03-25 -
通讯作者:Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li -
基金资助:We are grateful to the Germplasm Bank of Wild Species at the Kunming Institute of Botany (KIB) and Molecular Biology Experiment Center, Germplasm Bank of Wild Species for facilitating this study. This research was supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No: 2017eLSFGBOWSe02). We thank Dr. Chun-Lei Xiang for reviewing the first draft for us.
Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)
Hong Wua,b, Peng-Fei Maa, Hong-Tao Lia, Guo-Xiong Huc, De-Zhu Lia
- a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b University of Chinese Academy of Sciences, Beijing, 100049, China;
c College of Life Sciences, Guizhou University, Guiyang, Guizhou, 550025, China
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Received:2020-02-05Revised:2020-07-13Online:2021-02-25Published:2021-03-25 -
Contact:Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li -
Supported by:We are grateful to the Germplasm Bank of Wild Species at the Kunming Institute of Botany (KIB) and Molecular Biology Experiment Center, Germplasm Bank of Wild Species for facilitating this study. This research was supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No: 2017eLSFGBOWSe02). We thank Dr. Chun-Lei Xiang for reviewing the first draft for us.
摘要： Salvia is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. Salvia subg. Glutinaria, native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of Salvia (14 newly sequenced and 5 previously published). Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of Salvia are highly conserved, and IR contraction only occurred in two species (Salvia mekongensis and S. rosmarinus). In Salvia, sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia, suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of Salvia, resolving the interspecific relationship of Salvia subg. Glutinaria. The newly sequenced plastid genomes will also enrich the plastome database of Salvia, providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.
引用本文
Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li. Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)[J]. Plant Diversity, 2021, 43(01): 15-26.
Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li. Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)[J]. Plant Diversity, 2021, 43(01): 15-26.
表1 台湾海峡鱼类目、科、属和种的组成
Table 1 Compositions of order, family, genus and species of fishes in Taiwan Strait
| 纲 Class | 目 Order | 科 Family | 属 Genus | 种 Species |
|---|---|---|---|---|
| 数量 Numbers (%) | 数量 Numbers (%) | 数量 Numbers (%) | ||
| 盲鳗纲 Myxini | 盲鳗目 Myxiniformes | 1 (0.49) | 2 (0.27) | 8 (0.47) |
| 软骨鱼纲 Chondrichthyes | 银鲛目 Chimaeriformes | 1 (0.49) | 1 (0.14) | 1 (0.06) |
| 虎鲨目 Heterodontiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 须鲨目 Orectolobiformes | 4 (1.95) | 4 (0.54) | 6 (0.35) | |
| 鼠鲨目 Lamniformes | 4 (1.95) | 4 (0.54) | 4 (0.24) | |
| 真鲨目 Carcharhiniformes | 6 (2.93) | 19 (2.57) | 32 (1.88) | |
| 六鳃鲨目 Hexanchiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 角鲨目 Squaliformes | 2 (0.98) | 2 (0.27) | 4 (0.24) | |
| 扁鲨目 Squatiniformes | 1 (0.49) | 1 (0.14) | 4 (0.24) | |
| 电鳐目 Torpediniformes | 2 (0.98) | 5 (0.68) | 9 (0.53) | |
| 锯鳐目 Pristiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 鳐目 Rajiformes | 5 (2.44) | 8 (1.08) | 14 (0.82) | |
| 鲼目 Myliobatiformes | 3 (1.46) | 10 (1.36) | 25 (1.47) | |
| 辐鳍鱼纲 Actinopterygii | 鲟形目 Acipenseriformes | 1 (0.49) | 1 (0.14) | 1 (0.06) |
| 海鲢目 Elopiformes | 2 (0.98) | 2 (0.27) | 3 (0.18) | |
| 北梭鱼目 Albuliformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 鳗鲡目 Anguilliformes | 8 (3.90) | 34 (4.59) | 85 (5.01) | |
| 鲱形目 Clupeiformes | 4 (1.95) | 21 (2.83) | 49 (2.89) | |
| 鼠鱚目 Gonorynchiformes | 2 (0.98) | 2 (0.27) | 2 (0.12) | |
| 鲶形目 Siluriformes | 2 (0.98) | 4 (0.54) | 4 (0.24) | |
| 水珍鱼目 Argentiniformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 胡瓜鱼目 Osmeriformes | 1 (0.49) | 3 (0.41) | 5 (0.29) | |
| 巨口鱼目 Stomiiformes | 2 (0.98) | 8 (1.08) | 8 (0.47) | |
| 辫鱼目 Ateleopodiformes | 1 (0.49) | 2 (0.27) | 2 (0.12) | |
| 仙女鱼目 Aulopiformes | 5 (2.44) | 8 (1.08) | 24 (1.41) | |
| 灯笼鱼目 Myctophiformes | 2 (0.98) | 3 (0.41) | 4 (0.24) | |
| 月鱼目 Lampriformes | 3 (1.46) | 5 (0.68) | 5 (0.29) | |
| 鳕形目 Gadiformes | 3 (1.46) | 6 (0.81) | 15 (0.88) | |
| 鼬鳚目 Ophidiiformes | 2 (0.98) | 7 (0.95) | 8 (0.47) | |
| 鮟鱇目 Lophiiformes | 5 (2.44) | 9 (1.22) | 16 (0.94) | |
| 鲻形目 Mugiliformes | 1 (0.49) | 5 (0.68) | 11 (0.65) | |
| 银汉鱼目 Atheriniformes | 1 (0.49) | 2 (0.27) | 4 (0.24) | |
| 颌针鱼目 Beloniformes | 3 (1.46) | 14 (1.89) | 30 (1.77) | |
| 金眼鲷目 Beryciformes | 4 (1.95) | 8 (1.08) | 19 (1.12) | |
| 海鲂目 Zeiformes | 2 (0.98) | 3 (0.41) | 3 (0.18) | |
| 刺鱼目 Gasetrosteiformes | 6 (2.93) | 16 (2.16) | 31 (1.83) | |
| 鲉形目 Scorpaeniformes | 9 (4.39) | 50 (6.76) | 90 (5.30) | |
| 鲈形目 Perciformes | 85(41.46) | 383 (51.76) | 978 (57.63) | |
| 鲽形目 Pleuronectiformes | 9 (4.39) | 40 (5.41) | 98 (5.75) | |
| 鲀形目 Tetraodontiformes | 9 (4.39) | 43 (5.81) | 90 (5.30) | |
| 合计 Total | 40 | 206 (100.0) | 740 (100.0) | 1,697 (100.0) |
表1 台湾海峡鱼类目、科、属和种的组成
Table 1 Compositions of order, family, genus and species of fishes in Taiwan Strait
| 纲 Class | 目 Order | 科 Family | 属 Genus | 种 Species |
|---|---|---|---|---|
| 数量 Numbers (%) | 数量 Numbers (%) | 数量 Numbers (%) | ||
| 盲鳗纲 Myxini | 盲鳗目 Myxiniformes | 1 (0.49) | 2 (0.27) | 8 (0.47) |
| 软骨鱼纲 Chondrichthyes | 银鲛目 Chimaeriformes | 1 (0.49) | 1 (0.14) | 1 (0.06) |
| 虎鲨目 Heterodontiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 须鲨目 Orectolobiformes | 4 (1.95) | 4 (0.54) | 6 (0.35) | |
| 鼠鲨目 Lamniformes | 4 (1.95) | 4 (0.54) | 4 (0.24) | |
| 真鲨目 Carcharhiniformes | 6 (2.93) | 19 (2.57) | 32 (1.88) | |
| 六鳃鲨目 Hexanchiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 角鲨目 Squaliformes | 2 (0.98) | 2 (0.27) | 4 (0.24) | |
| 扁鲨目 Squatiniformes | 1 (0.49) | 1 (0.14) | 4 (0.24) | |
| 电鳐目 Torpediniformes | 2 (0.98) | 5 (0.68) | 9 (0.53) | |
| 锯鳐目 Pristiformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 鳐目 Rajiformes | 5 (2.44) | 8 (1.08) | 14 (0.82) | |
| 鲼目 Myliobatiformes | 3 (1.46) | 10 (1.36) | 25 (1.47) | |
| 辐鳍鱼纲 Actinopterygii | 鲟形目 Acipenseriformes | 1 (0.49) | 1 (0.14) | 1 (0.06) |
| 海鲢目 Elopiformes | 2 (0.98) | 2 (0.27) | 3 (0.18) | |
| 北梭鱼目 Albuliformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 鳗鲡目 Anguilliformes | 8 (3.90) | 34 (4.59) | 85 (5.01) | |
| 鲱形目 Clupeiformes | 4 (1.95) | 21 (2.83) | 49 (2.89) | |
| 鼠鱚目 Gonorynchiformes | 2 (0.98) | 2 (0.27) | 2 (0.12) | |
| 鲶形目 Siluriformes | 2 (0.98) | 4 (0.54) | 4 (0.24) | |
| 水珍鱼目 Argentiniformes | 1 (0.49) | 1 (0.14) | 1 (0.06) | |
| 胡瓜鱼目 Osmeriformes | 1 (0.49) | 3 (0.41) | 5 (0.29) | |
| 巨口鱼目 Stomiiformes | 2 (0.98) | 8 (1.08) | 8 (0.47) | |
| 辫鱼目 Ateleopodiformes | 1 (0.49) | 2 (0.27) | 2 (0.12) | |
| 仙女鱼目 Aulopiformes | 5 (2.44) | 8 (1.08) | 24 (1.41) | |
| 灯笼鱼目 Myctophiformes | 2 (0.98) | 3 (0.41) | 4 (0.24) | |
| 月鱼目 Lampriformes | 3 (1.46) | 5 (0.68) | 5 (0.29) | |
| 鳕形目 Gadiformes | 3 (1.46) | 6 (0.81) | 15 (0.88) | |
| 鼬鳚目 Ophidiiformes | 2 (0.98) | 7 (0.95) | 8 (0.47) | |
| 鮟鱇目 Lophiiformes | 5 (2.44) | 9 (1.22) | 16 (0.94) | |
| 鲻形目 Mugiliformes | 1 (0.49) | 5 (0.68) | 11 (0.65) | |
| 银汉鱼目 Atheriniformes | 1 (0.49) | 2 (0.27) | 4 (0.24) | |
| 颌针鱼目 Beloniformes | 3 (1.46) | 14 (1.89) | 30 (1.77) | |
| 金眼鲷目 Beryciformes | 4 (1.95) | 8 (1.08) | 19 (1.12) | |
| 海鲂目 Zeiformes | 2 (0.98) | 3 (0.41) | 3 (0.18) | |
| 刺鱼目 Gasetrosteiformes | 6 (2.93) | 16 (2.16) | 31 (1.83) | |
| 鲉形目 Scorpaeniformes | 9 (4.39) | 50 (6.76) | 90 (5.30) | |
| 鲈形目 Perciformes | 85(41.46) | 383 (51.76) | 978 (57.63) | |
| 鲽形目 Pleuronectiformes | 9 (4.39) | 40 (5.41) | 98 (5.75) | |
| 鲀形目 Tetraodontiformes | 9 (4.39) | 43 (5.81) | 90 (5.30) | |
| 合计 Total | 40 | 206 (100.0) | 740 (100.0) | 1,697 (100.0) |
表2 台湾海峡不同生态类型和栖息地鱼类种类数组成
Table 2 Habitat type and ecological characteristics of fishes in Taiwan Strait
| 适温性 Temperature adaptability | 栖息地生态类型 Habitat type | ||||||
|---|---|---|---|---|---|---|---|
| 大陆架砂泥质底层种类 Continental sandy- muddy demersal fish | 大陆架近底层种类 Continental benthopelagic fish | 大陆架中上层种类 Continental pelagic- neritic fish | 岩礁性鱼类 Reef- associated fish | 大洋性种类 Oceanic fish | 总种类数Total species | ||
| 暖水性种类 Warm water | 520 | 219 | 139 | 588 | 94 | 1,560 | |
| 暖温性种类 Warm temperate | 68 | 29 | 19 | 8 | 4 | 128 | |
| 冷温性种类 Cold temperate | 8 | 1 | 0 | 0 | 0 | 9 | |
| 总种类数 Total species | 596 | 249 | 158 | 596 | 98 | 1,697 | |
表2 台湾海峡不同生态类型和栖息地鱼类种类数组成
Table 2 Habitat type and ecological characteristics of fishes in Taiwan Strait
| 适温性 Temperature adaptability | 栖息地生态类型 Habitat type | ||||||
|---|---|---|---|---|---|---|---|
| 大陆架砂泥质底层种类 Continental sandy- muddy demersal fish | 大陆架近底层种类 Continental benthopelagic fish | 大陆架中上层种类 Continental pelagic- neritic fish | 岩礁性鱼类 Reef- associated fish | 大洋性种类 Oceanic fish | 总种类数Total species | ||
| 暖水性种类 Warm water | 520 | 219 | 139 | 588 | 94 | 1,560 | |
| 暖温性种类 Warm temperate | 68 | 29 | 19 | 8 | 4 | 128 | |
| 冷温性种类 Cold temperate | 8 | 1 | 0 | 0 | 0 | 9 | |
| 总种类数 Total species | 596 | 249 | 158 | 596 | 98 | 1,697 | |
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