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Luo L, Ye P, Lin Q, Liu M, Hao G, Wei T, Sahu SK. From sequences to sustainability: Exploring dipterocarp genomes for oleoresin production, timber quality, and conservation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112139. [PMID: 38838990 DOI: 10.1016/j.plantsci.2024.112139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/23/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
Dipterocarp species dominate tropical forest ecosystems and provide key ecological and economic value through their use of aromatic resins, medicinal chemicals, and high-quality timber. However, habitat loss and unsustainable logging have endangered many Dipterocarpaceae species. Genomic strategies provide new opportunities for both elucidating the molecular pathways underlying these desirable traits and informing conservation efforts for at-risk taxa. This review summarizes the progress in dipterocarp genomics analysis and applications. We describe 16 recently published Dipterocarpaceae genome sequences, representing crucial genetic blueprints. Phylogenetic comparisons delineate evolutionary relationships among species and provide frameworks for pinpointing functional changes underlying specialized metabolism and wood development patterns. We also discuss connections revealed thus far between specific gene families and both oleoresin biosynthesis and wood quality traits-including the identification of key terpenoid synthases and cellulose synthases likely governing pathway flux. Moreover, the characterization of adaptive genomic markers offers vital resources for supporting conservation practices prioritizing resilient genotypes displaying valuable oleoresin and timber traits. Overall, progress in dipterocarp functional and comparative genomics provides key tools for addressing the intertwined challenges of preserving biodiversity in endangered tropical forest ecosystems while sustainably deriving aromatic chemicals and quality lumber that support diverse human activities.
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Affiliation(s)
- Liuming Luo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Peng Ye
- College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Gang Hao
- College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China.
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Chase MW, Samuel R, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae). ANNALS OF BOTANY 2023; 131:123-142. [PMID: 35029647 PMCID: PMC9904355 DOI: 10.1093/aob/mcac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia. METHODS We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. KEY RESULTS RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. CONCLUSIONS The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.
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Affiliation(s)
- Mark W Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - John G Conran
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Felipe Nollet
- Universidade Federal Rural de Pernambuco, Centro de Ciências Biológicas, Departamento de Botânica, Rua Manuel de Medeiros, S/N, Dois Irmãos, 52171-900 Recife, Pernambuco, Brazil
| | - Paul Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aljaž Jakob
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Gabriel Vignolle
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Maria Teresa Buril
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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5
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Tian Z, Zeng P, Lu X, Zhou T, Han Y, Peng Y, Xiao Y, Zhou B, Liu X, Zhang Y, Yu Y, Li Q, Zong H, Zhang F, Jiang H, He J, Cai J. Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis. PLANT COMMUNICATIONS 2022; 3:100464. [PMID: 36303430 PMCID: PMC9700207 DOI: 10.1016/j.xplc.2022.100464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/26/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Dipterocarpoideae, the largest subfamily of the Dipterocarpaceae, is a dominant component of Southeast Asian rainforests and is widely used as a source of wood, damar resin, medicine, and essential oil. However, many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human disturbance. Genetic information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes, providing clues to the function and evolution of these species. Here, we report on 13 high-quality Dipterocarpoideae genome assemblies, ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in Dipterocarpoideae. Molecular dating analyses support the Western Gondwanaland origin of Dipterocarpaceae. Based on evolutionary analysis, we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 chromosomes. We discovered an expansion of genes encoding cellulose synthase (CesA), which is essential for cellulose biosynthesis and secondary cell-wall formation. We functionally identified five bornyl diphosphate synthase (BPPS) genes, which specifically catalyze the biosynthesis of borneol, a natural medicinal compound extracted from damar resin and oils, thus providing a basis for large-scale production of natural borneol in vitro.
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Affiliation(s)
- Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Xiaoyun Lu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yunxue Xiao
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kuming 650223, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xue Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yongting Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qiong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Feining Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Juan He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
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6
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Okuno S, Yin T, Nanami S, Matsuyama S, Kamiya K, Tan S, Davies SJ, Mohamad M, Yamakura T, Itoh A. Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species‐rich rainforest in Borneo. Ecol Evol 2022; 12:e9536. [DOI: 10.1002/ece3.9536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Seiya Okuno
- Graduate School of Science Osaka City University Osaka Japan
| | - Tingting Yin
- Graduate School of Science Osaka City University Osaka Japan
| | - Satoshi Nanami
- Graduate School of Science Osaka City University Osaka Japan
- Graduate School of Science Osaka Metropolitan University Osaka Japan
| | - Shuhei Matsuyama
- College of Agriculture, Food and Environmental Sciences Rakuno Gakuen University Ebetsu Japan
| | - Koichi Kamiya
- Graduate School of Agriculture Ehime University Matsuyama Japan
| | - Sylvester Tan
- Global Earth Observatory (ForestGEO) Smithsonian Tropical Research Institute Washington USA
| | - Stuart J. Davies
- Global Earth Observatory (ForestGEO) Smithsonian Tropical Research Institute Washington USA
| | | | - Takuo Yamakura
- Graduate School of Science Osaka City University Osaka Japan
| | - Akira Itoh
- Graduate School of Science Osaka City University Osaka Japan
- Graduate School of Science Osaka Metropolitan University Osaka Japan
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7
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Tang L, Liao X, Tembrock LR, Ge S, Wu Z. A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae). DNA Res 2022; 29:6529388. [PMID: 35171284 PMCID: PMC8882376 DOI: 10.1093/dnares/dsac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/12/2022] [Indexed: 11/23/2022] Open
Abstract
Vatica mangachapoi is a tropical tree species native to Southeast Asia. It has long been valued as a timber species because the wood resists decay, but it is now considered vulnerable to extinction due to habitat loss and overexploitation. Here, we present the first chromosome-level genome assembly of V. mangachapoi that we created by combining data from PacBio long read sequencing with Hi-C proximity ligation and Illumina short-read sequencing. The assembled genome was 456.21 Mb, containing 11 chromosome and a BUSCO score of 93.4%. From the newly assembled genome, 46,811 protein-coding genes were predicted. Repetitive DNA accounted for 53% of the genome. Phylogenomic and gene family analyses showed that V. mangachapoi diverged from a common ancestor of Gossypium raimondii 70 million years ago. Transcriptome analyses found 227 genes that were differentially expressed in the leaves of plants grown in normal soil relative to plants grown in dry, coastal, sandy soil. For these genes, we identified three significantly enriched with GO terms: responses to organonitrogen compounds, chitin-triggered immunity, and wound response. This genome provides an important comparative benchmark not only for future conservation work on V. mangachapoi but also for phylogenomics work on Dipterocarpaceae.
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Affiliation(s)
- Liang Tang
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University , Haikou, Hainan 570228, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen , Shenzhen 518120, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University , Fort Collins, CO 80523, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen , Shenzhen 518120, China
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8
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Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
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Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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9
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Chang YH, Yao G, Neilsen J, Liu DT, Zhang L, Ma YP. Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan (China), based on morphological and genomic data. PLANT DIVERSITY 2021; 43:292-298. [PMID: 34485771 PMCID: PMC8390914 DOI: 10.1016/j.pld.2021.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 05/20/2023]
Abstract
Rhododendron kuomeianum Y.H. Chang, J. Nielsen & Y.P. Ma, a new species of Rhododendron (Ericaceae) within subsect. Maddenia in sect. Rhododendron from Yiliang County, NE Yunnan, China, is described and illustrated. The new species is similar to R. valentinianum, but it can be easily distinguished by its sparse scales on the abaxial surface of the leaf blade, fewer flowers per inflorescence and white corolla with pale red margins. There are also differences in the widths of calyx lobes, leaf blade shape and indumentum characteristics of the petiole between the new species and Rhododendron linearilobum. We confirmed that R. kuomeianum is a new species closely related to R. valentinianum and R. changii with phylogenomic studies of 10 species within this subsection based on restriction site-associated DNA sequencing (RAD-seq) data. These phylogenomic analyses also clarified additional taxonomic problems in this subsection previously raised by morphological analysis. Our findings make a strong case for using next-generation sequencing to explore phylogenetic relationships and identify new species, especially in plants groups with complicated taxonomic problems.
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Affiliation(s)
- Yu-Hang Chang
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gang Yao
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jens Neilsen
- Dobbies Garden Centre, UK-DD2 Perth, Scotland, UK
| | - De-Tuan Liu
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lu Zhang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650051, China
| | - Yong-Peng Ma
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Corresponding author. Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Ahmad M, Leroy T, Krigas N, Temsch EM, Weiss-Schneeweiss H, Lexer C, Sehr EM, Paun O. Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb. FRONTIERS IN PLANT SCIENCE 2021; 12:706574. [PMID: 34335669 PMCID: PMC8317432 DOI: 10.3389/fpls.2021.706574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 06/08/2023]
Abstract
Background and Aims: Quantifying genetic variation is fundamental to understand a species' demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
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Affiliation(s)
- Muhammad Ahmad
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eva Maria Sehr
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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11
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Cvetković T, Areces-Berazain F, Hinsinger DD, Thomas DC, Wieringa JJ, Ganesan SK, Strijk JS. Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l. G3-GENES GENOMES GENETICS 2021; 11:6248091. [PMID: 33892500 PMCID: PMC8496235 DOI: 10.1093/g3journal/jkab136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/11/2021] [Indexed: 11/22/2022]
Abstract
Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage /Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into /Byttneriina (/Grewioideae +/Byttnerioideae) and /Malvadendrina. Within /Malvadendrina, /Helicteroideae occupied the earliest branching position, followed by /Sterculioideae, /Brownlowioideae, /Tiliodeae, and /Dombeyoideae formed a clade sister to /Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.
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Affiliation(s)
- Tijana Cvetković
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Biodiversity Genomics Team, Guangxi University, Daxuedonglu 100, Nanning, Guangxi, 530005, China
| | - Fabiola Areces-Berazain
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Herbarium UPRRP, Department of Biology, University of Puerto Rico, San Juan PR 00925-2537, United States of America
| | - Damien D Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000 Evry, France
| | - Daniel C Thomas
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
| | - Santhana K Ganesan
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Joeri S Strijk
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam
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12
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Dellinger AS. Pollination syndromes in the 21 st century: where do we stand and where may we go? THE NEW PHYTOLOGIST 2020; 228:1193-1213. [PMID: 33460152 DOI: 10.1111/nph.16793] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/31/2020] [Indexed: 06/12/2023]
Abstract
Pollination syndromes, recurring suites of floral traits appearing in connection with specific functional pollinator groups, have served for decades to organise floral diversity under a functional-ecological perspective. Some potential caveats, such as over-simplification of complex plant-animal interactions or lack of empirical observations, have been identified and discussed in recent years. Which of these caveats do indeed cause problems, which have been solved and where do future possibilities lie? I address these questions in a review of the pollination-syndrome literature of 2010 to 2019. I show that the majority of studies was based on detailed empirical pollinator observations and could reliably predict pollinators based on a few floral traits such as colour, shape or reward. Some traits (i.e. colour) were less reliable in predicting pollinators than others (i.e. reward, corolla width), however. I stress that future studies should consider floral traits beyond those traditionally recorded to expand our understanding of mechanisms of floral evolution. I discuss statistical methods suitable for objectively analysing the interplay of system-specific evolutionary constraints, pollinator-mediated selection and adaptive trade-offs at microecological and macroecological scales. I exemplify my arguments on an empirical dataset of floral traits of a neotropical plant radiation in the family Melastomataceae.
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13
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Brandrud MK, Baar J, Lorenzo MT, Athanasiadis A, Bateman RM, Chase MW, Hedrén M, Paun O. Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae). Syst Biol 2020; 69:91-109. [PMID: 31127939 PMCID: PMC6902629 DOI: 10.1093/sysbio/syz035] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 12/04/2022] Open
Abstract
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.
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Affiliation(s)
- Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Maria T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Alexander Athanasiadis
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | | | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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14
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Carneiro de Melo Moura C, Brambach F, Jair Hernandez Bado K, Krutovsky KV, Kreft H, Tjitrosoedirdjo SS, Siregar IZ, Gailing O. Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra. PLANTS 2019; 8:plants8110461. [PMID: 31671512 PMCID: PMC6918277 DOI: 10.3390/plants8110461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022]
Abstract
DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.
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Affiliation(s)
- Carina Carneiro de Melo Moura
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Fabian Brambach
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany.
| | - Kevin Jair Hernandez Bado
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany.
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Str., Moscow 119333, Russian.
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia.
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA.
| | - Holger Kreft
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany.
| | | | - Iskandar Z Siregar
- Department of Silviculture, Faculty of Forestry, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia.
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany.
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15
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Sramkó G, Paun O, Brandrud MK, Laczkó L, Molnár A, Bateman RM. Iterative allogamy-autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae). ANNALS OF BOTANY 2019; 124:481-497. [PMID: 31231754 PMCID: PMC6798847 DOI: 10.1093/aob/mcz103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/19/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing. METHODS We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample. KEY RESULTS The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine, is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams. CONCLUSIONS This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine, which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams.
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Affiliation(s)
- Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Debrecen, Hungary
- For correspondence. E-mail
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Levente Laczkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Attila Molnár
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
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16
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Cvetković T, Hinsinger DD, Strijk JS. Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing. Sci Rep 2019; 9:11639. [PMID: 31406227 PMCID: PMC6690942 DOI: 10.1038/s41598-019-48240-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/01/2019] [Indexed: 11/09/2022] Open
Abstract
Tropical forests, a key-category of land ecosystems, are faced with the world's highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae are one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae, and thus changes in habitat ecology, community composition and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genome. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinatus, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed low level of genomic diversity among analysed range-edge species, and different evolutionary history of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics and evolutionary studies.
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Affiliation(s)
- Tijana Cvetković
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China
| | - Damien Daniel Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000, Luang Prabang, Lao PDR
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, 530005, P.R. China.
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000, Luang Prabang, Lao PDR.
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17
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Herrando-Moraira S, Calleja JA, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Massó S, Montes-Moreno N, Roquet C, Sáez L, Sennikov A, Susanna A, Vilatersana R. Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework. Mol Phylogenet Evol 2019; 137:313-332. [DOI: 10.1016/j.ympev.2019.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/04/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023]
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18
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Záveská E, Maylandt C, Paun O, Bertel C, Frajman B, The Steppe Consortium, Schönswetter P. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae). Mol Phylogenet Evol 2019; 139:106572. [PMID: 31351183 DOI: 10.1016/j.ympev.2019.106572] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems.
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Affiliation(s)
- Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Clemens Maylandt
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Clara Bertel
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - The Steppe Consortium
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria; Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria; Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain; Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy; Institute for Alpine Environment, Eurac Research, Drususallee 1/Viale Druso 1, 39100 Bozen/Bolzano, Italy
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria.
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19
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Olmstead RG, Bedoya AM. Whole genomes: the holy grail. A commentary on: 'Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastidgenomes'. ANNALS OF BOTANY 2019; 123:iv-v. [PMID: 31106809 PMCID: PMC6526312 DOI: 10.1093/aob/mcz055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This article comments on: Jacqueline Heckenhauer, Ovidiu Paun, Mark W. Chase, Peter S. Ashton, A.S. Kamariah and Rosabelle Samuel. 2019. Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes. Annals of Botany 123(5): 857–865.
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Affiliation(s)
| | - Ana M Bedoya
- Department of Biology, University of Washington, Seattle, WA, USA
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20
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Heckenhauer J, Paun O, Chase MW, Ashton PS, Kamariah AS, Samuel R. Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes. ANNALS OF BOTANY 2019; 123:857-865. [PMID: 30541053 PMCID: PMC6526321 DOI: 10.1093/aob/mcy220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/12/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. METHODS A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. KEY RESULTS Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). CONCLUSIONS Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.
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Affiliation(s)
- Jacqueline Heckenhauer
- University of Vienna, Department of Botany and Biodiversity Research, Vienna, Austria
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Ovidiu Paun
- University of Vienna, Department of Botany and Biodiversity Research, Vienna, Austria
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Bently, WA, Australia
| | - Peter S Ashton
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - A S Kamariah
- University of Brunei Darussalam, Environmental and Life Sciences, Faculty of Science, Gadong, Brunei Darussalam
| | - Rosabelle Samuel
- University of Vienna, Department of Botany and Biodiversity Research, Vienna, Austria
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