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Teixidor-Toneu I, Westengen O, Ulian T, McMillion A, Lorimer M, Grace O, Caillon S, Shrestha P, Kool A. Co-conserving Indigenous and local knowledge systems with seeds. TRENDS IN PLANT SCIENCE 2023; 28:1370-1378. [PMID: 37479569 DOI: 10.1016/j.tplants.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/23/2023]
Abstract
Indigenous and local knowledge (ILK) holders have deep ecological, horticultural, and practical knowledge of plants, but this knowledge is not routinely considered and supported along with seed collections conserved ex situ. In this opinion, conceived collaboratively by a team of botanists, ecologists, ethnobiologists, and practitioners in biodiversity and ILK systems conservation, we propose seven actions towards the co-conservation of seeds and associated knowledge to overcome obstacles and encourage ex situ conservation institutions to support knowledge holders in multiple ways. Success depends on simultaneous changes in conservation practices, new collaborative relationships, and shifts in policy to share and conserve biocultural diversity. Failure to act will witness the continued erosion of ILK and depreciation of ex situ plant collections.
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Affiliation(s)
- Irene Teixidor-Toneu
- IMBE, Aix Marseille University, Avignon University, CNRS, IRD, Marseille, France; Natural History Museum, University of Oslo, Oslo, Norway.
| | | | - Tiziana Ulian
- Royal Botanic Gardens, Kew, Wellcome Trust Millennium Building, Wakehurst, UK
| | | | - Matthias Lorimer
- European Coordination Let's Liberate Diversity!, Brussels, Belgium
| | - Olwen Grace
- Royal Botanic Gardens, Kew, Richmond, UK; Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Sophie Caillon
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Montpellier, France
| | - Pitambar Shrestha
- Local Initiatives for Biodiversity, Research, and Development (LI-BIRD), Pokhara, Nepal
| | - Anneleen Kool
- Natural History Museum, University of Oslo, Oslo, Norway.
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Quatela AS, Cangren P, Jafari F, Michel T, de Boer HJ, Oxelman B. Retrieval of long DNA reads from herbarium specimens. AOB PLANTS 2023; 15:plad074. [PMID: 38130422 PMCID: PMC10735254 DOI: 10.1093/aobpla/plad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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Affiliation(s)
- Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Farzaneh Jafari
- Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran
- Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Thibauld Michel
- Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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Le HTT, Nguyen LN, Pham HLB, Le HTM, Luong TD, Huynh HTT, Nguyen VT, Nong HV, Teixidor-Toneu I, De Boer HJ, Manzanilla V. Target Capture Reveals the Complex Origin of Vietnamese Ginseng. FRONTIERS IN PLANT SCIENCE 2022; 13:814178. [PMID: 35909770 PMCID: PMC9326450 DOI: 10.3389/fpls.2022.814178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/21/2022] [Indexed: 05/30/2023]
Abstract
The global market of the medicinal plant ginseng is worth billions of dollars. Many ginseng species are threatened in the wild and effective sustainable development initiatives are necessary to preserve biodiversity at species and genetic level whilst meeting the demand for medicinal produce. This is also the case of Panax vietnamensis Ha & Grushv., an endemic and threatened ginseng species in Vietnam that is locally cultivated at different scales and has been the object of national breeding programs. To investigate the genetic diversity within cultivated and wild populations of P. vietnamensis we captured 353 nuclear markers using the Angiosperm-353 probe set. Genetic diversity and population structure were evaluated for 319 individuals of Vietnamese ginseng across its area of distribution and from wild and a varying range of cultivated areas. In total, 319 individuals were sampled. After filtering, 1,181 SNPs were recovered. From the population statistics, we observe high genetic diversity and high genetic flow between populations. This is also supported by the STRUCTURE analysis. The intense gene flow between populations and very low genetic differentiation is observed regardless of the populations' wild or cultivated status. High levels of admixture from two ancestral populations exist in both wild and cultivated samples. The high gene flow between populations can be attributed to ancient and on-going practices of cultivation, which exist in a continuum from understorey, untended breeding to irrigated farm cultivation and to trade and exchange activities. These results highlight the importance of partnering with indigenous peoples and local communities and taking their knowledge into account for biodiversity conservation and sustainable development of plants of high cultural value.
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Affiliation(s)
- Hien Thi Thu Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
| | - Linh Nhat Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hang Le Bich Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hao Thi My Le
- Soils and Fertilizers Research Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Toan Duc Luong
- Soils and Fertilizers Research Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Hue Thi Thu Huynh
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
| | - Van Tuong Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hai Van Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
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Ramdayal M, Maat H, van Andel T. The legacy of traditional rice cultivation by descendants of Indian contract laborers in Suriname. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2021; 17:60. [PMID: 34663358 PMCID: PMC8524977 DOI: 10.1186/s13002-021-00485-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/05/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Some 35,000 indentured laborers from India were recruited to work on plantations in Suriname between 1868 and 1916. It is likely that most were familiar with farming before they were shipped to this former Dutch colony in the Caribbean. Around 1900, those who did not return received a piece of land where most of them started growing rice as a staple crop. Agronomists characterized their traditional landraces as inferior and infested with weedy rice and started to 'purify' these landraces. No research has been done on whether these ancient rice varieties still exist. We aimed to document the rice varieties (both landraces and more modern cultivars) grown currently or in the recent past by (descendants of) Hindustani smallholders in Suriname, their origin, morphological and agronomic characters, local uses and cultural and spiritual relevance. Given the rapid decline in small-scale rice cultivation in the past 40 years, we wanted to know why people continued or abandoned rice farming and what aspects of traditional practices still survived. METHODS We interviewed 26 (former) small-scale Hindustani farmers and asked about the varieties they cultivated and traditional agricultural practices. We collected seed samples, local names and associated information, and compared these to information from agricultural reports from the colonial period. We also interviewed 11 Maroons, one Javanese farmer, and three persons of mixed ethnicity, who were somehow involved in the cultivation of East Indian rice varieties. RESULTS AND DISCUSSION Hindustani smallholders in Suriname largely lost their traditional rice landraces. Most of the interviewed farmers grew modern cultivars, developed after 2000. Some cultivars from the 1950s were still planted for fodder, but these were heavily mixed with weedy rice and other weeds. Maroon farmers in the interior, however, still actively cultivated varieties with names like 'coolie rice', which probably descend from landraces introduced by the Indian contract laborers, although this needs to be confirmed by molecular research. Although traditional cultivation practices seem to have been lost, smallholders still retain pleasant memories of the manual planting, harvesting, and processing of rice, as well as the gender-based practices and beliefs associated with the cultivation of the crop. The oral history of former rice farmers and traditional rice varieties (possibly obtained from Maroon fields) could play a role in museum settings as living vehicles for memories of the descendants of Asian contract labourers in Suriname and Guyana.
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Affiliation(s)
- Melissa Ramdayal
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Harro Maat
- Social Science Department, Wageningen University, Wageningen, The Netherlands
| | - Tinde van Andel
- Institute of Biology, Leiden University, Leiden, The Netherlands.
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands.
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Ufimov R, Zeisek V, Píšová S, Baker WJ, Fér T, van Loo M, Dobeš C, Schmickl R. Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11442. [PMID: 34336405 PMCID: PMC8312748 DOI: 10.1002/aps3.11442] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/09/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. METHODS To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony-informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. RESULTS Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. DISCUSSION A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.
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Affiliation(s)
- Roman Ufimov
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
- Komarov Botanical InstituteRussian Academy of Sciencesul. Prof. Popova 2St. Petersburg197376Russian Federation
| | - Vojtěch Zeisek
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
| | - Soňa Píšová
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
| | | | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
| | - Christoph Dobeš
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
| | - Roswitha Schmickl
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
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McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt‐Lebuhn AN, Baker WJ, Forest F, Jackson CJ. New targets acquired: Improving locus recovery from the Angiosperms353 probe set. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311420. [PMID: 34336399 PMCID: PMC8312740 DOI: 10.1002/aps3.11420] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.
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Affiliation(s)
- Todd G. B. McLay
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
- Centre for Australian National Biodiversity ResearchCSIROCanberraAustralia
| | - Joanne L. Birch
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Bee F. Gunn
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Weixuan Ning
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Jennifer A. Tate
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lars Nauheimer
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Elizabeth M. Joyce
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Lalita Simpson
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Chris J. Jackson
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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Siniscalchi CM, Hidalgo O, Palazzesi L, Pellicer J, Pokorny L, Maurin O, Leitch IJ, Forest F, Baker WJ, Mandel JR. Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311422. [PMID: 34336403 PMCID: PMC8312747 DOI: 10.1002/aps3.11422] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. METHODS We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. RESULTS Our results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. DISCUSSION Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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Affiliation(s)
- Carolina M. Siniscalchi
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
| | - Oriane Hidalgo
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Luis Palazzesi
- División PaleobotánicaMuseo Argentino de Ciencias NaturalesCONICETBuenos AiresC1405DJRArgentina
| | - Jaume Pellicer
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIAPozuelo de Alarcón (Madrid)28223Spain
| | - Olivier Maurin
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Felix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | | | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Hu Y, Huang Y, Zhou S, Zhang Y, Cheng R, Guo J, Ling Y. Traditional rice landraces in Lei-Qiong area of South China tolerate salt stress with strong antioxidant activity. PLANT SIGNALING & BEHAVIOR 2020; 15:1740466. [PMID: 32180487 PMCID: PMC7194380 DOI: 10.1080/15592324.2020.1740466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Salt stress, causing serious loss on crop productions, is one of the most important environmental stresses throughout the world. The aim of this study is to select salt-tolerant traditional rice resources collected from Lei-Qiong area of South China and investigate their physiological performances and biochemical regulations during salt stress response, together with two well-known international varieties, Nona Bokra (salt-tolerant sample) and IR29 (salt-sensitive sample). After comprehensive analyses, we discovered that two Lei-Qiong traditional salt-tolerant rice samples showed less growth inhibition by salt stress during both germination and seedling stage, in comparison with other rice samples. Moreover, there were less chlorosis symptoms in these two kinds of salt tolerant rice under salt stress, corresponding to their better water-holding capacity. We measured malondialdehyde and proline contents, and activities of CAT and POD of seedlings treated with 100 mM NaCl for 5 dand 10 d, respectively. Interestingly, less cellular membrane damage and stronger antioxidant enzyme system were found in the two Lei-Qiong rice samples. Our study suggests that traditional rice landrace growing onshore of Lei-Qiong area in China possesses good salt-tolerant capacity, which could be attributed to their efficient antioxidant enzyme system.
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Affiliation(s)
- Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Shuangxi Zhou
- New Zealand Institute for Plant and Food Research Limited, Hawkes Bay, New Zealand
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Risheng Cheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
- CONTACT Jianfu Guo
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
- Yu Ling College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088 PR China
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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