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Wang R, Lan Z, Luo Y, Deng Z. The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species. Sci Rep 2024; 14:8523. [PMID: 38609472 PMCID: PMC11014926 DOI: 10.1038/s41598-024-59132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with traditional practices, facilitating the scientific validation of ancient remedies. This integration enhances public understanding of traditional Chinese medicine's efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs or small shrubs, exhibiting simple petiolate or sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering the precise identification and taxonomic elucidation of Stachys species. To address this gap, we assembled the complete chloroplast (CP) genome of Stachys geobombycis and conducted reannotation and comparative analysis of seven additional species within the Stachys genus. The findings demonstrate that the CP genomes of these species exhibit quadripartite structures, with lengths ranging from 14,523 to 150,599 bp. Overall, the genome structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding genes, 36 tRNA genes, and 8 rRNA genes. Additionally, 78 to 98 SSRs and long repeat sequences were detected , and notably, 6 highly variable regions were identified as potential molecular markers in the CP genome through sequence alignment. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Stachys as a member of Stachydeae tribe. Overall, this comprehensive bioinformatics study of Stachys CP genomes lays the groundwork for phylogenetic classification, plant identification, genetic engineering, evolutionary studies, and breeding research concerning medicinal plants within the Stachys genus.
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Affiliation(s)
- Ru Wang
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yongjian Luo
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
- Central South University of Forestry and Technology, Key Laboratory of Forestry Biotechnology of Hunan Province, Changsha, 410000, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China.
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2
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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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3
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Xue L, Cai JH, Zhan M, Li XP, Wu L, Chen YP. Molecular and morphological evidence for a new species of Stachys (Lamiaceae) from Hunan, China. PHYTOKEYS 2023; 236:121-134. [PMID: 38312773 PMCID: PMC10838187 DOI: 10.3897/phytokeys.236.112741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/26/2023] [Indexed: 02/06/2024]
Abstract
Stachysyingzuijieensis, a new species from western Hunan, China, is described and illustrated. Molecular phylogenetic analyses based on three nuclear ribosomal DNA loci (ETS, ITS and 5S-NTS) recovered S.yingzuijieensis within the Stachys clade and as a sister group of S.arrecta. The two species can be easily distinguished by the morphology of lamina, corolla and nutlet. A key to all species of Stachydeae from China is also provided.
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Affiliation(s)
- Ling Xue
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China Central South University of Forestry and Technology Changsha China
| | - Jia-Hua Cai
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China Central South University of Forestry and Technology Changsha China
| | - Min Zhan
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China Central South University of Forestry and Technology Changsha China
| | - Xiao-Ping Li
- Yingzuijie National Nature Reserve of Hunan Province, Huaihua 563517, China Yingzuijie National Nature Reserve of Hunan Province Huaihua China
| | - Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China Central South University of Forestry and Technology Changsha China
| | - Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
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Acha S, Linan A, MacDougal J, Edwards C. The evolutionary history of vines in a neotropical biodiversity hotspot: Phylogenomics and biogeography of a large passion flower clade (Passiflora section Decaloba). Mol Phylogenet Evol 2021; 164:107260. [PMID: 34273502 DOI: 10.1016/j.ympev.2021.107260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
Because of their extraordinary flower and leaf morphology, passion flowers (Passifloraceae) have fascinated naturalists since their discovery. Within the large, diverse (600 species) genus Passiflora is an especially enigmatic and species-rich (120 spp.) subclade, Section Decaloba, which occurs in the Neotropics and has its center of diversity in Andean montane forests. A recent phylogenetic study of Passifloraceae showed that Section Decaloba was monophyletic, but was unable to resolve relationships within the clade, thus preventing inferences of evolutionary history and biogeography. The goal of this study was to elucidate the phylogeny and biogeography of Section Decaloba. We sampled 206 accessions representing 91 of the ~ 120 known species in section Decaloba and four outgroups, with samples derived predominantly from herbarium specimens. We generated DNA sequences using a high-throughput DNA sequencing technique called 2b-RAD, reconstructed the phylogeny, and conducted ancestral area reconstructions to infer the biogeographic history of the group. We recovered predominantly well-supported trees in which species were grouped into two main clades: 1) the Central American clade, within which the majority of nodes well supported and species were monophyletic and 2) the South American clade, a large clade that showed overall lower resolution and included several polyphyletic species and species complexes that need additional research. RASP analysis showed that section Decaloba originated in Central America around 10.4 Ma, and then dispersed to South America, the Greater Antilles, and the Bahamas. The South American clade diversified in the Northern Andes and then dispersed to the rest of South America, and Lesser Antilles. Results suggest that both long-distance dispersal and colonization of newly available habitats (i.e., in the Andes) likely promoted diversification of this clade. This study also illustrates how using herbarium specimens and a RAD-seq approach can produce phylogenies for broadly distributed, highly diverse, and poorly accessible groups of plants where field collections would be unfeasible.
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Affiliation(s)
- Serena Acha
- Department of Biology, University of Missouri-St. Louis, One University Blvd, Research Hall St. Louis, MO 63121, USA; Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA; University of Florida Herbarium, Florida Museum of Natural History,1659 Museum Rd, Gainesville, FL 32611-7800, USA.
| | - Alexander Linan
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA
| | - John MacDougal
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA; Harris-Stowe State University, 3026 Laclede Ave, St. Louis, MO 63103, USA
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5
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Zhao F, Chen YP, Salmaki Y, Drew BT, Wilson TC, Scheen AC, Celep F, Bräuchler C, Bendiksby M, Wang Q, Min DZ, Peng H, Olmstead RG, Li B, Xiang CL. An updated tribal classification of Lamiaceae based on plastome phylogenomics. BMC Biol 2021; 19:2. [PMID: 33419433 PMCID: PMC7796571 DOI: 10.1186/s12915-020-00931-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. RESULTS We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. CONCLUSIONS Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification.
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Affiliation(s)
- Fei Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yasaman Salmaki
- Center of Excellence in Phylogeny of Living Organisms, Department of Plant Science, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 68849, USA
| | - Trevor C Wilson
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, Turkey
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010, Wien, Austria
| | - Mika Bendiksby
- NTNU University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Qiang Wang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinense Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Dao-Zhang Min
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Bo Li
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Huang W, Gao X, Zhang Y, Jin C, Wang X. The complete chloroplast genome sequence of stachys sieboldii Miquel. (Labiatae), a kind of vegetable crop and Chinese medicinal material plant. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1751006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Weinan Huang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiang Gao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyu Zhang
- College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Chaoge Jin
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianguo Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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7
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Abrahamczyk S. Comparison of the ecology and evolution of plants with a generalist bird pollination system between continents and islands worldwide. Biol Rev Camb Philos Soc 2019; 94:1658-1671. [DOI: 10.1111/brv.12520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Stefan Abrahamczyk
- Nees‐Institute for Biodiversity of PlantsUniversity of Bonn 53115 Bonn Germany
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8
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Ouyang P, Kang D, Mo X, Tian E, Hu Y, Huang R. Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing. Molecules 2018; 23:molecules23082014. [PMID: 30104467 PMCID: PMC6222658 DOI: 10.3390/molecules23082014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/16/2018] [Accepted: 08/05/2018] [Indexed: 11/16/2022] Open
Abstract
Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10⁻40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.
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Affiliation(s)
- Puyue Ouyang
- Agricultural College, Guangxi University, Nanning 530005, China.
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou 510520, China.
| | - Dali Kang
- College of Medical Technology, Ningbo College of Health Sciences, Ningbo 315100, China.
| | - Xiaolu Mo
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou 510520, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Yanyu Hu
- Agricultural College, Guangxi University, Nanning 530005, China.
| | - Rongshao Huang
- Agricultural College, Guangxi University, Nanning 530005, China.
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Identification of Insecticidal Constituents from the Essential Oil from the Aerial Parts Stachys riederi var. japonica. Molecules 2018; 23:molecules23051200. [PMID: 29772795 PMCID: PMC6099633 DOI: 10.3390/molecules23051200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 11/17/2022] Open
Abstract
The essential oil of Stachys riederi var. japonica (Family: Lamiaceae) was extracted by hydrodistillation and determined by GC and GC-MS. A total of 40 components were identified, representing 96.01% of the total oil composition. The major compounds in the essential oil were acetanisole (15.43%), anisole (9.43%), 1,8-cineole (8.07%), geraniol (7.89%), eugenol (4.54%), caryophyllene oxide (4.47%), caryophyllene (4.21%) and linalool (4.07%). Five active constituents (acetanisole, anisole, 1,8-cineole, eugenol and geraniol) were identified by bioactivity-directed fractionation. The essential oil possessed fumigant toxicity against maize weevils (Sitophilus zeamais) and booklice (Liposcelis bostrychophila), with LC50 values of 15.0 mg/L and 0.7 mg/L, respectively. Eugenol and anisole exhibited stronger fumigant toxicity than the oil against booklice. 1,8-Cineole showed stronger toxicity, and anisole as well as eugenol exhibited the same level of fumigant toxicity as the essential oil against maize weevils. The essential oil also exhibited contact toxicity against S. zeamais adults and L. bostrychophila, with LC50 values of 21.8 µg/adult and 287.0 µg/cm², respectively. The results indicated that the essential oil of S. riederi var. japonica and its isolates show potential as fumigants, and for their contact toxicity against grain storage insects.
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Levin DA, Scarpino SV. On the young age of intraspecific herbaceous taxa. THE NEW PHYTOLOGIST 2017; 213:1513-1520. [PMID: 27726173 DOI: 10.1111/nph.14224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX 78713, USA
| | - Samuel V Scarpino
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT 05401, USA
- Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification. Sci Rep 2016; 6:34343. [PMID: 27748362 PMCID: PMC5066227 DOI: 10.1038/srep34343] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/13/2016] [Indexed: 11/26/2022] Open
Abstract
Lamiaceae, the sixth largest angiosperm family, contains more than 7000 species distributed all over the world. However, although considerable progress has been made in the last two decades, its phylogenetic backbone has never been well resolved. In the present study, a large-scale phylogenetic reconstruction of Lamiaceae using chloroplast sequences was carried out with the most comprehensive sampling of the family to date (288 species in 191 genera, representing approximately 78% of the genera of Lamiaceae). Twelve strongly supported primary clades were inferred, which form the phylogenetic backbone of Lamiaceae. Six of the primary clades correspond to the current recognized subfamilies Ajugoideae, Lamioideae, Nepetoideae, Prostantheroideae, Scutellarioideae, and Symphorematoideae, and one corresponds to a portion of Viticoideae. The other five clades comprise: 1) Acrymia and Cymaria; 2) Hymenopyramis, Petraeovitex, Peronema, and Garrettia; 3) Premna, Gmelina, and Cornutia; 4) Callicarpa; and 5) Tectona. Based on these results, three new subfamilies—Cymarioideae, Peronematoideae, and Premnoideae—are described, and the compositions of other subfamilies are updated based on new findings from the last decade. Furthermore, our analyses revealed five strongly supported, more inclusive clades that contain subfamilies, and we give them phylogenetically defined, unranked names: Cymalamiina, Scutelamiina, Perolamiina, Viticisymphorina, and Calliprostantherina.
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12
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Roy T, Catlin NS, Garner DMG, Cantino PD, Scheen AC, Lindqvist C. Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci. PeerJ 2016; 4:e2220. [PMID: 27547537 PMCID: PMC4958014 DOI: 10.7717/peerj.2220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nathan S Catlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Biology, University of Florida, Gainesville, FL, United States
| | - Drake M G Garner
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
| | - Philip D Cantino
- Department of Environmental and Plant Biology, Ohio University , Athens , OH , United States
| | | | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
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13
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The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol 2016; 99:16-33. [DOI: 10.1016/j.ympev.2016.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
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14
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Gaudeul M, Véla E, Rouhan G. Eastward colonization of the Mediterranean Basin by two geographically structured clades: The case of Odontites Ludw. (Orobanchaceae). Mol Phylogenet Evol 2016; 96:140-149. [DOI: 10.1016/j.ympev.2015.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/09/2015] [Accepted: 12/14/2015] [Indexed: 11/16/2022]
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15
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Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae). Mol Phylogenet Evol 2016; 98:184-200. [PMID: 26923493 DOI: 10.1016/j.ympev.2016.01.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 01/19/2016] [Accepted: 01/29/2016] [Indexed: 11/22/2022]
Abstract
Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai-Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.
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Roy T, Lindqvist C. New insights into evolutionary relationships within the subfamily Lamioideae (Lamiaceae) based on pentatricopeptide repeat (PPR) nuclear DNA sequences. AMERICAN JOURNAL OF BOTANY 2015; 102:1721-1735. [PMID: 26451039 DOI: 10.3732/ajb.1500233] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Lamioideae, one of the most species-rich subfamilies within Lamiaceae, exhibits a remarkable diversity in morphology and habit and is found in many temperate to subtropical regions across the globe. Previous studies based on chloroplast DNA (cpDNA) sequence data produced a tribal classification of Lamioideae, but so far this has not been confirmed with nuclear DNA loci. METHODS We investigated sequence variation in a low-copy nuclear pentatricopeptide repeat (PPR) region and compared the phylogenetic results with previously published sequence data from a concatenated data set comprising four cpDNA loci. We incorporated representatives of all 10 lamioid tribes and some unclassified taxa, analyzed the data using phylogenetic inference, and estimated divergence times and ancestral areas for major nodes. KEY RESULTS Our results showed overall topological similarities between the cpDNA and PPR phylogenies with strong support for most tribes. However, we also observed incongruence in the circumscription of some tribes, including Gomphostemmateae and Pogostemoneae and in the relationships among tribes. Our results suggest an Oligocene-Miocene origin of the Lamioideae crown group. Asia and the Mediterranean region appear to have been centers of diversity and place of origin for many lamioid tribes. CONCLUSIONS This study represents the first phylogeny of subfamily Lamioideae inferred from low-copy nuclear DNA data. We show that most lamioid tribes are corroborated, although the exact circumscription of two tribes is questioned. We have shed further light on the evolutionary relationships within Lamioideae, and this study demonstrates the utility of the PPR region for such subfamilial-level phylogenetic studies.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, New York 14260 USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, New York 14260 USA
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Viale E, Martinez-Sañudo I, Brown JM, Simonato M, Girolami V, Squartini A, Bressan A, Faccoli M, Mazzon L. Pattern of association between endemic Hawaiian fruit flies (Diptera, Tephritidae) and their symbiotic bacteria: Evidence of cospeciation events and proposal of "Candidatus Stammerula trupaneae". Mol Phylogenet Evol 2015; 90:67-79. [PMID: 25959751 DOI: 10.1016/j.ympev.2015.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 04/18/2015] [Accepted: 04/28/2015] [Indexed: 11/18/2022]
Abstract
Several insect lineages have evolved mutualistic association with symbiotic bacteria. This is the case of some species of mealybugs, whiteflies, weevils, tsetse flies, cockroaches, termites, carpenter ants, aphids and fruit flies. Some species of Tephritinae, the most specialized subfamily of fruit flies (Diptera: Tephritidae), harbour co-evolved vertically transmitted, bacterial symbionts in their midgut, known as "Candidatus Stammerula spp.". The 25 described endemic species of Hawaiian tephritids, plus at least three undescribed species, are taxonomically distributed among three genera: the cosmopolitan genus Trupanea (21 described spp.), the endemic genus Phaeogramma (2 spp.) and the Nearctic genus Neotephritis (2 spp.). We examined the presence of symbiotic bacteria in the endemic tephritids of the Hawaiian Islands, which represent a spectacular example of adaptive radiation, and tested the concordant evolution between host and symbiont phylogenies. We detected through PCR assays the presence of specific symbiotic bacteria, designated as "Candidatus Stammerula trupaneae", from 35 individuals of 15 species. The phylogeny of the insect host was reconstructed based on two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII), while the bacterial 16S rRNA was used for the symbiont analysis. Host and symbiont phylogenies were then compared and evaluated for patterns of cophylogeny and strict cospeciation. Topological congruence between Hawaiian Tephritinae and their symbiotic bacteria phylogenies suggests a limited, but significant degree of host-symbiont cospeciation. We also explored the character reconstruction of three host traits, as island location, host lineage, and host tissue attacked, based on the symbiont phylogenies under the hypothesis of cospeciation.
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Affiliation(s)
- E Viale
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
| | - I Martinez-Sañudo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
| | - J M Brown
- Department of Biology, Grinnell College, Grinnell, IA 50012, USA.
| | - M Simonato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
| | - V Girolami
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy
| | - A Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
| | - A Bressan
- Bayer Crop Science LP, R&D Trait Research, 3500 Paramount Parkway, Morrisville, NC 27560, USA.
| | - M Faccoli
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
| | - L Mazzon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova - Agripolis, Viale dell'Università, 16, 35020 Legnaro, Padova, Italy.
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Roy T, Cole LW, Chang TH, Lindqvist C. Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phylogenet Evol 2015; 89:46-62. [PMID: 25888973 DOI: 10.1016/j.ympev.2015.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 02/05/2023]
Abstract
The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Logan W Cole
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
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Salmaki Y, Zarre S, Ryding O, Lindqvist C, Bräuchler C, Heubl G, Barber J, Bendiksby M. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae). Mol Phylogenet Evol 2013; 69:535-51. [PMID: 23916621 DOI: 10.1016/j.ympev.2013.07.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/20/2013] [Accepted: 07/23/2013] [Indexed: 11/26/2022]
Abstract
Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid-nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae.
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Affiliation(s)
- Yasaman Salmaki
- Center of Excellence in Phylogeny of Living Organisms, Department of Plant Science, College of Science, University of Tehran, PO Box 14155-6455, Tehran, Iran; Biodiversity Research - Systematic Botany, Department of Biology I, Ludwig-Maximilians Universität München, Menzinger Str. 67, D-80638 München, Germany.
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