1
|
Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
Collapse
Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
2
|
Li Z, Duan B, Zhou Z, Fang H, Yang M, Xia C, Zhou Y, Wang J. Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing. BMC Genomics 2024; 25:39. [PMID: 38191291 PMCID: PMC10773089 DOI: 10.1186/s12864-023-09920-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/17/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Scutellaria baicalensis Georgi has been extensively used as a medicinal herb in China for over 2000 years. They may be intentionally or inadvertently substituted or blended with comparable species in the local market, threatening clinical medication safety. Molecular markers are effective tools to prevent misidentification and eliminate doping and falsification among Scutellaria plants. This study screened four highly variable regions to identify Scutellaria and its adulterants. In addition, a phylogenetic analysis was performed using the complete cp genome combined with published Scutellaria species samples. Moreover, a comparative analysis of the cp genomes was conducted to investigate the cp genome evolution of S. baicalensis. RESULTS The complete cp genome of five species of Scutellaria was sequenced for the first time, and four previously published Scutellaria species were re-sequenced. They all exhibited a conserved quadripartite structure in their cp genomes, including two distinct regions, namely a small and large single copy region, respectively, and two inverted repeats encompassing the majority of ribosomal RNA genes. Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. Four highly variable regions (matK-rps16, ndhC-trnV-UAC, psbE-petL, and rps16-trnQ-UUG) may function as potential molecular markers for differentiating S. baicalensis from its adulterants. Additionally, the monophyly of Scutellaria was ascertained and could be reclassified into two subgenera, subgenus Anaspis and subgenus Scutellaria, as evidenced by the phylogenetic analyses on sequences of cp genome and shared protein-coding sequences. According to the molecular clock analysis, it has been inferred that the divergence of Scutellaria occurred at approximately 4.0 Mya during the Pliocene Epoch. CONCLUSION Our study provides an invaluable theoretical basis for further Scutellaria species identification, phylogenetics, and evolution analysis.
Collapse
Affiliation(s)
- Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, 133002, China
| | - Hui Fang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Ying Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Institute of Caulis Dendrobii of Longling County, Baoshan, 678300, China.
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| |
Collapse
|
3
|
Chang J, Nakamura K, Chao C, Luo M, Liao P. Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta. Ecol Evol 2023; 13:e10435. [PMID: 37600490 PMCID: PMC10439367 DOI: 10.1002/ece3.10435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages ("ghost introgression"). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference-based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re-evaluating the evolutionary independency of cryptic lineages, the group-wise diverged single-nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.
Collapse
Affiliation(s)
- Jui‐Tse Chang
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chien‐Ti Chao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Min‐Xin Luo
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Pei‐Chun Liao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| |
Collapse
|
4
|
Jiang Y, Zhu C, Wang S, Wang F, Sun Z. Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode. Sci Rep 2023; 13:5602. [PMID: 37019975 PMCID: PMC10075158 DOI: 10.1038/s41598-023-32493-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
Scutellaria baicalensis has been one of the most commonly used traditional Chinese medicinal plants in China for more than 2000 years. The three new varieties cultivated could not be distinguished by morphology before flowering. It will hinder the promotion of later varieties. Chloroplast DNA has been widely used in species identification. Moreover, previous studies have shown that complete chloroplast genome sequences have been suggested as super barcodes for identifying plants. Therefore, we sequenced and annotated the complete chloroplast genomes of three cultivated varieties. The chloroplast genomes of SBW, SBR, and SBP were 151,702 bp, 151,799 bp, and 151,876 bp, which contained 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The analysis of the repeat sequences, codon usage, and comparison of chloroplast genomes shared a high degree of conservation. However, the sliding window results show significant differences among the three cultivated varieties in matK-rps16 and petA-psbJ. And we found that the matK-rps16 sequence can be used as a barcode for the identification of three varieties. In addition, the complete chloroplast genome contains more variations and can be used as a super-barcode to identify these three cultivated varieties. Based on the protein-coding genes, the phylogenetic tree demonstrated that SBP was more closely related to SBW, in the three cultivated varieties. Interestingly, we found that S. baicalensis and S. rehderiana are closely related, which provides new ideas for the development of S. baicalensis. The divergence time analysis showed that the three cultivated varieties diverged at about 0.10 Mya. Overall, this study showed that the complete chloroplast genome could be used as a super-barcode to identify three cultivated varieties of S. baicalensis and provide biological information, and it also contributes to bioprospecting.
Collapse
Affiliation(s)
- Yuan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chenghao Zhu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shangtao Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Fusheng Wang
- Dingxi Academy of Agricultural Sciences, Dingxi, China.
| | - Zhirong Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
| |
Collapse
|
5
|
Morphological and Genetic Diversity of Scutellaria tuvensis Juz., an Endemic of Desert Steppes. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
For the first time, an assessment of phenotypic variability and genetic polymorphism was performed on endemic plants Scutellaria tuvensis Juz. growing in Tuva (five populations; Russia). Based on morphological traits of individuals, principal component analysis clustered the individuals into three groups depending on characteristics of their habitats: group 1 turned out to be sampled from beach gravel, group 2 from a detrital cone, and group 3 from coarse rock fragments; this finding was confirmed by specific features of the development of the individuals in these habitats. Using inter-simple sequence repeat markers, high genetic polymorphism was identified at the population level: the proportion of polymorphic loci was 95%, expected heterozygosity 0.221, the absolute number of alleles 1.533, and the effective number of alleles 1.376. Population 3 (P 3) was the most genetically homogeneous; P 5 was characterized by the highest genetic diversity. In an unweighted pair group method with arithmetic mean dendrogram, the studied populations formed two major groups: the first cluster included P 4 and P 5, and the second cluster contained plants collected in P 1, P 2, and P 3. An analysis of the population structure using the STRUCTURE software showed the same result, dividing the sample under study into two subpopulations. The genetic differentiation index among populations was 0.232, and gene flow 1.655. According to analysis of molecular variance, intrapopulation differences accounted for 73% of total genetic diversity.
Collapse
|
6
|
Shen J, Li P, Liu S, Liu Q, Li Y, Sun Y, He C, Xiao P. Traditional uses, ten-years research progress on phytochemistry and pharmacology, and clinical studies of the genus Scutellaria. JOURNAL OF ETHNOPHARMACOLOGY 2021; 265:113198. [PMID: 32739568 DOI: 10.1016/j.jep.2020.113198] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/08/2020] [Accepted: 07/17/2020] [Indexed: 05/27/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Scutellaria (Lamiaceae), which includes approximately 360-469 accepted species, is widespread in Europe, North America, East Asia, and South America. Several species have a long history being used as traditional medicines to treat respiratory, peptic, neurological, and hepatic and gall diseases. The phytochemistry and pharmacology of the genus Scutellaria have been developed dramatically in the past ten years, and the traditional uses and clinical studies of the genus have not been systematically summarized. Therefore, it is especially valuable to review the current state of knowledge to provide a basis for further exploration of its medicinal potential. AIM OF THE REVIEW The review aims to provide updated information on the ethnopharmacology, the ten-year research progress of phytochemistry and pharmacology, and clinical studies of Scutellaria and to explore the potential medicinal values and further studies of Scutellaria. MATERIALS AND METHODS This review is based on published studies and books from the library and electronic sources, including SciFinder, Scopus, PubMed, Web of Science, Baidu Scholar, CNKI, the online ethnobotanical database, and ethnobotanical monographs. This literature is related to ethnopharmacology, the ten-year research progress on the phytochemistry and pharmacology, and clinical studies of Scutellaria. RESULTS A total of 50 species, 5 subspecies and 17 varieties of the genus Scutellaria are used as traditional medicine with various biological activities. In the past ten years, 208 chemical constituents have been identified from 16 species and 1 variety of the genus Scutellaria, such as neo-clerodane diterpenoids, sesterterpenoids, terpenoids, flavonoids. Pharmacological research has demonstrated that the extracts and compounds identified from this genus exhibit extensive biological activities, including anticancer, antioxidant, anti-inflammatory, antiviral and antibacterial activities, effects on cardiovascular, cerebrovascular diseases as well as hepatoprotective and neuroprotective effects. The species S. baicalensis, S. barbata, and S. lateriflora and the main compounds baicalein, baicalin and wogonin are involved in clinical trials, which point the way for us to conduct further studies, such as study on the anticancer, antihypertensive, anti-infective, anti-inflammatory, neuroprotective and other effects of Scutellaria. CONCLUSIONS The species included in the genus Scutellaria can be used to treat cancer, infection, hepatic disorders, cardiovascular and cerebrovascular diseases, neurodegenerative diseases, and other diseases. Some indications in traditional medicines have been confirmed by modern pharmacological studies, such as anticancer, anti-inflammatory, anti-infective activity, and hepatoprotective and neuroprotective effects. The available literature indicated that most of the bioactivities could be attributed to flavonoids and neo-clerodane diterpenoids. Although there are some uses of Scutellaria in clinical practice, the existing research on this genus is still limited. In order to expand the development of medicinal resources of Scutellaria, the already studied species in this genus are recommended for more comprehensive investigation on their active substances, pharmacological mechanisms, quality control, clinical use and new drug research. Additionally, it is necessary to study species that their chemical composition or pharmacological activity have not yet been investigated, especially those used in folk medicine.
Collapse
Affiliation(s)
- Jie Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Pei Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Shuangshuang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Qing Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Yue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Yuhua Sun
- Xinjiang Institute of Materia Medica, Urumqi, 830004, China.
| | - Chunnian He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, China.
| |
Collapse
|
7
|
Yang J, Chiang YC, Hsu TW, Kim SH, Pak JH, Kim SC. Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. Sci Rep 2021; 11:1152. [PMID: 33441744 PMCID: PMC7806662 DOI: 10.1038/s41598-020-80143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
Collapse
Affiliation(s)
- JiYoung Yang
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, 1 Mingshen East Road, Chichi Township, Nantou, 55244, Taiwan
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Jae-Hong Pak
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Xu Z, Gao R, Pu X, Xu R, Wang J, Zheng S, Zeng Y, Chen J, He C, Song J. Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:230-240. [PMID: 33157301 PMCID: PMC7801248 DOI: 10.1016/j.gpb.2020.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/20/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023]
Abstract
Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication (WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.
Collapse
Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Ranran Gao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Rong Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Jiyong Wang
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Sihao Zheng
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Yan Zeng
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Jun Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Chunnian He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China.
| |
Collapse
|
10
|
Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, Liu ED, Salmaki Y, Peng H, Xiang CL. Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae). PLoS One 2020; 15:e0232602. [PMID: 32379799 PMCID: PMC7205251 DOI: 10.1371/journal.pone.0232602] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.
Collapse
Affiliation(s)
- Fei Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Li
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Bryan T. Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, United States of America
| | - Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qiang Wang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - En-De Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yasaman Salmaki
- Center of Excellence in Phylogeny of Living Organisms and Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
11
|
Chao CT, Huang BH, Chang JT, Liao PC. Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data. PHYTOKEYS 2020; 140:33-45. [PMID: 32148430 PMCID: PMC7052021 DOI: 10.3897/phytokeys.140.48578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
The genus Scutellaria comprises eight species distributed from 50 to 2000 m in Taiwan. Amongst them, S. barbata and S. taipeiensis are very similar on the basis of morphological and plastid DNA sequence information. Therefore, a comprehensive study of the taxonomic status of S. taipeiensis is necessary. We reviewed the herbarium sheets, related literature and protologues and compared morphologies of these two species, as well as their phylogenetic relationships. All evidence, including the diagnostic characters between S. taipeiensis and S. barbata, suggest that they belonged to a single species rather than two. As a result, S. taipeiensis is treated as a synonym of S. barbata.
Collapse
Affiliation(s)
- Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. 4 section, Wenshan District, Taipei City 116, TaiwanNational Taiwan Normal UniversityTaipei CityTaiwan
| | - Bing-Hong Huang
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. 4 section, Wenshan District, Taipei City 116, TaiwanNational Taiwan Normal UniversityTaipei CityTaiwan
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. 4 section, Wenshan District, Taipei City 116, TaiwanNational Taiwan Normal UniversityTaipei CityTaiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. 4 section, Wenshan District, Taipei City 116, TaiwanNational Taiwan Normal UniversityTaipei CityTaiwan
| |
Collapse
|
12
|
Genetic evidence of the southward founder speciation of Cycas taitungensis from ancestral C. revoluta along the Ryukyu Archipelagos. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01193-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
13
|
Yang CK, Chiang YC, Huang BH, Ju LP, Liao PC. Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands. BOTANICAL STUDIES 2018; 59:27. [PMID: 30406863 PMCID: PMC6223401 DOI: 10.1186/s40529-018-0244-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/31/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus. RESULTS Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate. CONCLUSIONS The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.
Collapse
Affiliation(s)
- Chih-Kai Yang
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
- The Experimental Forest, College of Bio-Resources and Agriculture, National Taiwan University, 12, Sec. 1, Chien-Shan Rd., Nantou, 55750 Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, 70, Lien-Hai Rd., Kaohsiung, 80424 Taiwan
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
| | - Li-Ping Ju
- Botanical Garden Division, Taiwan Forestry Research Institute, 53, Nan-Hai Rd., Taipei, 10066 Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
| |
Collapse
|
14
|
Zhang L, Zeng T, Hu H, Fan L, Zheng H, Hu Q. Interspecific Divergence of Two Sinalliaria (Brassicaceae) Species in Eastern China. FRONTIERS IN PLANT SCIENCE 2018; 9:77. [PMID: 29445389 PMCID: PMC5797776 DOI: 10.3389/fpls.2018.00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
How endemic species originated in eastern Asia has interested botanists for a long time. In this study, we combined experimental and computational modeling approaches to examine the morphological and genetic divergence and reproductive isolation of two tentative species of Sinalliaria (Brassicaceae) endemic to eastern China, S. limprichtiana and S. grandifolia. Most of the examined morphological characters (including hairs of leaf blades and stems, corolla length and width, and flower stalk length) were well-delineated between two species at the same ploidy level, and there was clear evidence of reproductive isolation between them (mainly due to post-pollination barriers) in the common garden environment. There were also strong and consistent divergences in the population genetic data. Coalescent simulations based on sequence variation of the nuclear genes suggest that interspecific divergence began during the Pleistocene when the climate oscillated in eastern Asia. Gene flow between two species appears to have been very limited and asymmetrical. Our results suggested that both species are well-differentiated and that the fast divergence between them might have been together shaped by both stochastic processes and habitat selection pressures.
Collapse
|
15
|
Unique parallel radiations of high-mountainous species of the genus Sedum (Crassulaceae) on the continental island of Taiwan. Mol Phylogenet Evol 2017; 113:9-22. [DOI: 10.1016/j.ympev.2017.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 02/02/2023]
|
16
|
Huang BH, Huang CW, Huang CL, Liao PC. Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants. Sci Rep 2017; 7:5465. [PMID: 28710389 PMCID: PMC5511155 DOI: 10.1038/s41598-017-05900-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/06/2017] [Indexed: 01/11/2023] Open
Abstract
Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson's metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.
Collapse
Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan.
| |
Collapse
|
17
|
Chen PC, Shih CH, Chu TJ, Lee YC, Tzeng TD. Phylogeography and genetic structure of the oriental river prawn Macrobrachium nipponense (Crustacea: Decapoda: Palaemonidae) in East Asia. PLoS One 2017; 12:e0173490. [PMID: 28267807 PMCID: PMC5340376 DOI: 10.1371/journal.pone.0173490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/21/2017] [Indexed: 11/25/2022] Open
Abstract
The oriental river prawn (Macrobrachium nipponense) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK). The nucleotide diversity (π) of all individuals was 0.01134, with values ranging from 0.0089 (BLJ, Japan) to 0.01425 (MTR, Taiwan). A total of 83 haplotypes were obtained, and the haplotypes were divided into 2 main lineages: lineage A included the specimens from BLJ, KLJ, CLR, MTR, TLC, MRC and JRC, and lineage B comprised the ones from HRK, SRC, SMR, MTR, TLC, MRC and JRC. Lineage A could be further divided two sub-lineages (A1 and A2). Individuals of lineage A2 were only from TLC. Demographic expansion was observed in each lineage, starting within the second-to-latest interglacial period for lineage A and within the last glacial period for lineage B. All FST values among the ten populations were significantly different, except for the values between MRC and JRC, and SMR and SRC. The phylogeography and genetic structure of M. nipponense in East Asia might be influenced by Pleistocene glacial cycles, lake isolation and human introduction. The possible dispersal routes of M. nipponense in the East Asia were also discussed.
Collapse
Affiliation(s)
- Po-Cheng Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chun-Han Shih
- Department of Leisure Management, Tungnan University, New Taipei City, Taiwan
| | - Ta-Jen Chu
- Department of Leisure and Recreation Management, Chung Hua University, Hsin Chu, Taiwan
| | - Ying-Chou Lee
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- * E-mail: (TDT); (YCL)
| | - Tzong-Der Tzeng
- Department of Leisure, Recreation and Tourism Management, Shu-Te University, Kaohsiung, Taiwan
- * E-mail: (TDT); (YCL)
| |
Collapse
|
18
|
Hsiung HY, Huang BH, Chang JT, Huang YM, Huang CW, Liao PC. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species. FRONTIERS IN PLANT SCIENCE 2017; 8:159. [PMID: 28239386 PMCID: PMC5301026 DOI: 10.3389/fpls.2017.00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.
Collapse
Affiliation(s)
- Huan-Yi Hsiung
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Jui-Tse Chang
- Department of Entomology, National Taiwan UniversityTaipei, Taiwan
| | - Yao-Moan Huang
- Division of Silviculture, Taiwan Forestry Research InstituteTaipei, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| |
Collapse
|
19
|
Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes. Sci Rep 2016; 6:39031. [PMID: 27966614 PMCID: PMC5155217 DOI: 10.1038/srep39031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/16/2016] [Indexed: 01/19/2023] Open
Abstract
Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
Collapse
Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| |
Collapse
|
20
|
Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species. BMC Evol Biol 2016; 16:191. [PMID: 27639694 PMCID: PMC5027097 DOI: 10.1186/s12862-016-0759-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower. RESULTS In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations. CONCLUSIONS Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species.
Collapse
Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Pingtung, Taiwan 91201 Republic of China
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, No.35, Tsinghua East Road, Beijing, 100083 China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
| |
Collapse
|
21
|
Tsai CC, Chou CH, Wang HV, Ko YZ, Chiang TY, Chiang YC. Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs. BMC PLANT BIOLOGY 2015; 15:202. [PMID: 26276316 PMCID: PMC4537552 DOI: 10.1186/s12870-015-0560-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/17/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA. RESULTS A pattern of vicariance, dispersal, and vicariance + dispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicariance + dispersal scenario, with geographic subdivision along Huxley's, Wallace's and Lydekker's Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM). CONCLUSIONS Taxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicariance + dispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.
Collapse
Affiliation(s)
- Chi-Chu Tsai
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Chang-Hung Chou
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
- Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan.
| | - Hao-Ven Wang
- Department of Life Science, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Science, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
| |
Collapse
|
22
|
Huang BH, Pang E, Chen YW, Cao H, Ruan Y, Liao PC. Positive selection and functional divergence of R2R3-MYB paralogous genes expressed in inflorescence buds of Scutellaria species (Labiatae). Int J Mol Sci 2015; 16:5900-21. [PMID: 25782156 PMCID: PMC4394512 DOI: 10.3390/ijms16035900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 02/15/2015] [Accepted: 03/05/2015] [Indexed: 11/25/2022] Open
Abstract
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification.
Collapse
Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd., Sec. 4, Taipei 116, Taiwan.
| | - Erli Pang
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, 1, Shuefu Rd., Neipu, Pingtung 912, Taiwan.
| | - Huifen Cao
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yu Ruan
- School of Life Science and Engineering, Chongqing Three Gorges University, Chongqing 404001, China.
- The College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd., Sec. 4, Taipei 116, Taiwan.
| |
Collapse
|