1
|
Chen C, Ruhfel BR, Li J, Wang Z, Zhang L, Zhang L, Mao X, Wang J, He D, Luo Y, Hu Q, Duan Y, Xu X, Xi Z, Liu J. Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36749624 DOI: 10.1111/jipb.13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.
Collapse
Affiliation(s)
- Chunlin Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Brad R Ruhfel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zefu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Dashan He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yue Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuanwen Duan
- Institute Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| |
Collapse
|
2
|
The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated. Proc Natl Acad Sci U S A 2022; 119:e2112737119. [PMID: 35617436 DOI: 10.1073/pnas.2112737119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceResilience is required to withstand or mitigate the effect of human-induced climate change. Today whole ecosystems are affected by climate change, but our understanding of their evolution and natural response is limited, often restricted to individual populations or species. The enigmatic flora on the tops of the African sky islands is isolated and unique, showing striking adaptations to the harsh tropical alpine conditions. Here we analyze genome data from a large fraction of afroalpine plants and show that this remarkable flora has a dynamic history with frequent colonizations and extinctions, most likely caused by previous natural climate changes during the ice-age cycles. The flora will be particularly vulnerable to human-induced climate warming, reducing alpine habitat into successively smaller areas.
Collapse
|
3
|
Feng Z, Zheng Y, Jiang Y, Miao YJ, Luo GM, Huang L. Complete chloroplast genome of Gentianopsis barbata and comparative analysis with related species from Gentianaceae. Genome 2022; 65:363-375. [DOI: 10.1139/gen-2021-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gentianopsis barbata is an essential medicinal plant in China with high ornamental and medicinal values. Unfortunately, the study of the chloroplast genome of this plant still has a gap. This study sequenced and characterized the complete chloroplast genome of G. barbata. The complete chloroplast genome of G. barbata is a typical circular structure with 151,123 bp. It consists of a large single-copy region (82,690 bp) and a small single-copy region (17,887 bp) separated by a pair of inverted repeats (25,273 bp), which covers 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Repeat analysis showed the highest frequency of palindrome. Thirty-seven simple sequence repeats were identified, most of which were single nucleotides. The bayesian inference tree, maximum likelihood tree, and neighbor joining tree suggested that G. barbata is grouped with Gentianopsis grandis and Gentianopsis paludosa. The divergence time analysis showed that G. barbata diverged at 1.243 Mya. Comparative chloroplast analysis can reveal interspecific diversity, and regions with high variation can be used to develop molecular markers applicable to various research areas. Our results provide new insight into plastome evolution and valuable resource for further studies on G. barbata.
Collapse
Affiliation(s)
- Zhan Feng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yan Zheng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yuan Jiang
- Chinese Academy of Medical Sciences & Peking Union Medical College, 12501, Beijing, China
- Dali University, 66359, Dali, China
| | - Yu Jing Miao
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
| | - Guang Ming Luo
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, China
| | - Linfang Huang
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, China
| |
Collapse
|
4
|
Biogeographical and Diversification Analyses of Indian Pseudoscorpions Reveal the Western Ghats as Museums of Ancient Biodiversity. Mol Phylogenet Evol 2022; 175:107495. [DOI: 10.1016/j.ympev.2022.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
|
5
|
Zhang Y, Yu J, Xia M, Chi X, Khan G, Chen S, Zhang F. Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau. Ecol Evol 2021; 11:16034-16046. [PMID: 34824809 PMCID: PMC8601884 DOI: 10.1002/ece3.8274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/07/2022] Open
Abstract
Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. The results revealed that the length of all plastome sequenced varied from 149 to 151 kb and have high similarity in structure and gene content. Phylogenomic analysis showed that Comastoma is a monophyletic group, closely related to the genus Lomatogonium. The divergence time estimation showed that Gentianaceae diverged at about 21.81 Ma, while the split of Comastoma occurred at 7.70 Ma. However, the results suggested the crown age of species formation in this genus is after 4.19 Ma. Our results suggest that QTP uplift, the alternation of Quaternary glaciation and interglaciation, and monsoon changes might have acted as drivers of speciation in Comastoma.
Collapse
Affiliation(s)
- Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Gulzar Khan
- Institute for Biology and Environmental SciencesCarl von Ossietzky‐University OldenburgOldenburgGermany
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| |
Collapse
|
6
|
Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL. Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AOB PLANTS 2021; 13:plaa068. [PMID: 33510891 PMCID: PMC7821390 DOI: 10.1093/aobpla/plaa068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 05/31/2023]
Abstract
The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centres of diversity for several alpine groups. Although it is known that the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary processes underlying diversity in this genus, especially the formation of narrow endemics, are still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal internal transcribed spacer sequence data. Genetic divergence within G. hoae ~3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.
Collapse
Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Hong-Yu Wang
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng-Xi Tan
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Xiao-Jun Zhou
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
| |
Collapse
|
7
|
Joshi J, Edgecombe GD. Evolutionary biogeography of the centipede genus Ethmostigmus from Peninsular India: testing an ancient vicariance hypothesis for Old World tropical diversity. BMC Evol Biol 2019; 19:41. [PMID: 30709332 PMCID: PMC6359765 DOI: 10.1186/s12862-019-1367-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/18/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Understanding the relative influence of vicariance and dispersal in shaping Old World tropical biodiversity remains a challenge. We aimed to infer the roles of these alternative biogeographic processes using a species time-tree for the centipede genus Ethmostigmus from the Old World tropics. Additionally, we explored fine-scale biogeographic patterns for an endemic radiation of Ethmostigmus from the peninsular Indian Plate (PIP), an area with complex geological and climatic history. RESULTS Divergence time estimates suggest that Ethmostigmus began diversifying in the Late Cretaceous, 99 (± 25) million years ago (Ma), its early biogeographic history shaped by vicariance. Members of Ethmostigmus in PIP form a monophyletic group that underwent endemic radiation in the Late Cretaceous, 72 (± 25) Ma. In contrast, a new species of Ethmostigmus from north-east India formed a clade with African/Australian species. Fine-scale biogeographic analyses in PIP predict that Indian Ethmostigmus had an ancestor in southern-central parts of the Western Ghats. This was followed by four independent dispersal events from the southern-central Western Ghats to the Eastern Ghats, and between different parts of the Western Ghats in the Cenozoic. CONCLUSIONS Our results are consistent with Gondwanan break-up driving the early evolutionary history of the genus Ethmostigmus. Multiple dispersal events coinciding with geo-climatic events throughout the Cenozoic shaped diversification in PIP. Ethmostigmus species in PIP are restricted to wet forests and have retained that niche throughout their diversification.
Collapse
Affiliation(s)
- Jahnavi Joshi
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | | |
Collapse
|
8
|
Fu PC, Ya HY, Liu QW, Cai HM, Chen SL. Out of Refugia: Population Genetic Structure and Evolutionary History of the Alpine Medicinal Plant Gentiana lawrencei var. farreri (Gentianaceae). Front Genet 2018; 9:564. [PMID: 30534138 PMCID: PMC6275180 DOI: 10.3389/fgene.2018.00564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic structure and evolutionary history of plants contributes to their conservation and utilization and helps to predict their response to environmental changes. The wildflower and traditional Chinese and Tibetan medicinal plant Gentiana lawrencei var. farreri is endemic to the Qinghai-Tibetan Plateau (QTP). To explore its genetic structure and evolutionary history, the genetic diversity, divergence, and demographics were analyzed in individuals from 31 locations across the QTP using 1 chloroplast marker and 10 nuclear microsatellite loci. High genetic diversity was detected in G. lawrencei var. farreri, and most of the genetic variance was found within populations. Values of F ST in G. lawrencei var. farreri from nuclear microsatellite and chloroplast data were 0.1757 and 0.739, respectively. The data indicated the presence of isolation by distance. The southeast edge of the QTP was the main refugium for G. lawrencei var. farreri, and one microrefugium was also detected in the plateau platform of the QTP. Both nuclear microsatellite and chloroplast data indicated that the populations were divided into two geographically structured groups, a southeast group and a northwest group. The current genetic pattern was mainly formed through recolonization from the two independent refugia. Significant melt was detected at the adjacent area of the two geographically structured groups. Approximate Bayesian computation showed that the northwest group had diverged from the southeast group, which then underwent population expansion. Our results suggest that the two-refugia pattern had a significant impact on the genetic structure and evolutionary history of G. lawrencei var. farreri.
Collapse
Affiliation(s)
- Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Hui-Yuan Ya
- College of Food and Drug, Luoyang Normal University, Luoyang, China
| | - Qi-Wei Liu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Hui-Min Cai
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| |
Collapse
|
9
|
Toussaint EF, Short AE. Transoceanic Stepping–stones between Cretaceous waterfalls? The enigmatic biogeography of pantropical Oocyclus cascade beetles. Mol Phylogenet Evol 2018; 127:416-428. [DOI: 10.1016/j.ympev.2018.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/07/2018] [Accepted: 04/15/2018] [Indexed: 10/17/2022]
|
10
|
High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes. Mol Phylogenet Evol 2018; 122:15-28. [PMID: 29360617 DOI: 10.1016/j.ympev.2018.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 11/14/2017] [Accepted: 01/13/2018] [Indexed: 11/27/2022]
Abstract
Lichen biodiversity and its generative evolutionary processes are practically unknown in the MIOI (Madagascar and Indian Ocean Islands) biodiversity hotspot. We sought to test the hypothesis that lichenized fungi in this region have undergone a rapid radiation, following a single colonization event, giving rise to narrow endemics, as is characteristic of other lineages of plants. We extensively sampled specimens of the lichen genus Sticta in the Mascarene archipelago (mainly Réunion) and in Madagascar, mainly in the northern range (Amber Mt and Marojejy Mt) and produced the fungal ITS barcode sequence for 148 thalli. We further produced a four-loci data matrix for 68 of them, representing the diversity and geographical distribution of ITS haplotypes. We reconstructed the phylogenetic relationships within this group, established species boundaries with morphological context, and estimated the date of the most recent common ancestor. Our inferences resolve a robust clade comprising 31 endemic species of Sticta that arose from the diversification following a single recent (c. 11 Mya) colonization event. All but three species have a very restricted range, endemic to either the Mascarene archipelago or a single massif in Madagascar. The first genus of lichens to be studied with molecular data in this region underwent a recent radiation, exhibits micro-endemism, and thus exemplifies the biodiversity characteristics found in other taxa in Madagascar and the Mascarenes.
Collapse
|
11
|
Sun SS, Fu PC, Zhou XJ, Cheng YW, Zhang FQ, Chen SL, Gao QB. The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:493. [PMID: 29765380 PMCID: PMC5938401 DOI: 10.3389/fpls.2018.00493] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/03/2018] [Indexed: 05/15/2023]
Abstract
The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa, to represent its three serious: ser. Ornatae, ser. Verticillatae, and ser. Monanthae. The cp genome sizes of the seven species ranged from 137,278 to 147,156 bp. The plastome size variation mainly occurred in the small single-copy and long single-copy regions rather than the inverted repeat regions. Compared with sect. Cruciata, the plastomes in ser. Ornatae and ser. Verticillatae had lost approximately 11 kb of sequences containing 11 ndh genes. Conversely, far fewer losses were observed in ser. Monanthae. The phylogenetic tree revealed that sect. Kudoa was not monophyletic and that ser. Monanthae was more closely related to other sections rather than sect. Kudoa. The molecular dating analysis indicated that ser. Monanthae and sect. Kudoa diverged around 8.23 Ma. In ser. Ornatae and ser. Verticillatae, the divergence occurred at around 0.07-1.78 Ma. The nucleotide diversity analysis indicated that the intergenic regions trnH-psbA, trnK-trnQ, ycf3-trnS and rpl32-trnL constituted divergence hotspots in both sect. Kudoa and Gentiana, and would be useful for future phylogenetic and population genetic studies.
Collapse
Affiliation(s)
- Shan-Shan Sun
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Xiao-Jun Zhou
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Yan-Wei Cheng
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
- *Correspondence: Qing-Bo Gao,
| |
Collapse
|
12
|
Toussaint EFA, Fikáček M, Short AEZ. India-Madagascar vicariance explains cascade beetle biogeography. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12791] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS USA
| | - Martin Fikáček
- Department of Entomology; National Museum; Cirkusova 1740, CZ-19800 Praha 9 Czech Republic
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7, CZ-12843 Praha 2 Czech Republic
| | - Andrew E. Z. Short
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS USA
| |
Collapse
|