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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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2
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Sato MP, Matsuo A, Otsuka K, Takano KT, Maki M, Okano K, Suyama Y, Ito‐Inaba Y. Potential contribution of floral thermogenesis to cold adaptation, distribution pattern, and population structure of thermogenic and non/slightly thermogenic Symplocarpus species. Ecol Evol 2023; 13:e10319. [PMID: 37456070 PMCID: PMC10349278 DOI: 10.1002/ece3.10319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
The genus Symplocarpus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of Symplocarpus contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic Symplocarpus renifolius and non/slightly thermogenic Symplocarpus nipponicus. ENM revealed that the distribution of S. nipponicus decreased, whereas that of S. renifolius expanded in the Last Glacial Maximum. Phylogeographic analyses have shown that the population structures of the two species were genetically segmented and that the genetic diversity of S. renifolius was higher than that of S. nipponicus. The phylogenetic relationship between chloroplast and nuclear DNA is topologically different in the two species, which may be due to the asymmetric gene flow ubiquitously observed in plants. The results of this study imply that floral thermogenesis of Symplocarpus contributes to expanding the distribution during an ice age, resulting in increased genetic diversity due to cold adaptation.
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Affiliation(s)
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural ScienceTohoku UniversityOsakiJapan
| | - Koichi Otsuka
- Tomono‐Kai Society of Nagano Environmental Conservation Research InstituteNaganoJapan
| | - Kohei Takenaka Takano
- Natural Environment DivisionNagano Environmental Conservation Research InstituteNaganoJapan
| | - Masayuki Maki
- Botanical GardensTohoku UniversitySendaiJapan
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Kunihiro Okano
- Department of Biological EnvironmentAkita Prefectural UniversityAkitaJapan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural ScienceTohoku UniversityOsakiJapan
| | - Yasuko Ito‐Inaba
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Department of Agricultural and Environmental Sciences, Faculty of AgricultureUniversity of MiyazakiMiyazakiJapan
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Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y. Molecular phylogeny and taxonomy of the Hydrangeaserrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H.acuminata from Yakushima. PHYTOKEYS 2022; 188:49-71. [PMID: 35095292 PMCID: PMC8770417 DOI: 10.3897/phytokeys.188.64259] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
According to the contemporary classification of Hydrangea native to Japan, H.serrata is a polymorphic species including six varieties. We discovered a plant identified as H.serrata, but morphologically distinct from previously known varieties, in Yakushima island where approximately 50 endemic species are known. To determine the relationship of this plant with previously known varieties, we examined morphology and constructed a highly resolved phylogeny of H.serrata and its relatives using three chloroplast genomic regions, rbcL, trnL intron, psbA-trnH, and two nuclear genomic regions, ITS1 and ITS2, and Multiplex ISSR genotyping by sequencing (MIG-seq). Based on these morphological and phylogenetic observations, we describe Hydrangeaacuminatasubsp.yakushimensissubsp. nov. as a newly discovered lineage in Yakushima, Japan and propose Hydrangeaminamitanii stat. nov. and Hydrangeaacuminatasubsp.australisstat. nov. which were previously treated as varieties of H.serrata.
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Affiliation(s)
- Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, JapanTohoku UniversityOsakiJapan
| | - Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819–0395, JapanKyushu Open UniversityFukuokaJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819–0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819–0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890–0065, JapanKagoshima UniversityKagoshimaJapan
| | - Shinji Fujii
- Department of Environmental Science, University of Human Environments, Okazaki, Aichi, 444–3505, JapanUniversity of Human EnvironmentsOkazakiJapan
| | | | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, JapanTohoku UniversityOsakiJapan
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Demeulenaere E, Schils T, Burleigh JG, Ringelberg JJ, Koenen EJM, Ickert-Bond SM. Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae). PHYTOKEYS 2022; 205:335-361. [PMID: 36762011 PMCID: PMC9849021 DOI: 10.3897/phytokeys.205.79144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/02/2022] [Indexed: 05/03/2023]
Abstract
The Indo-Pacific legume genus Serianthes was recently placed in the Archidendron clade (sensu Koenen et al. 2020), a subclade of the mimosoid clade in subfamily Caesalpinioideae, which also includes Acacia, Archidendron, Archidendropsis, Falcataria, Pararchidendron, Paraserianthes and Wallaceodendron. Serianthes comprises ca. 18 species, five subspecies and two varieties that are characterised by bipinnately compound leaves with alternate sessile leaflets, branched axillary corymbiform panicles and woody indehiscent pods. Generic relationships, as well as species relationships within genera in the Archidendron clade, remain uncertain. While the sister relationship between Serianthes and the genus Falcataria is strongly supported by molecular data, the distinction between Serianthes and the monotypic genus Wallaceodendron has been questioned, based on their similar flower and fruit morphologies. We combined three gene-enriched hybrid capture DNA sequence datasets (generated from the 964 mimobaits v1 probe set, the expanded 997 mimobaits v2 probe set and the GoFlag angiosperm 408 probe set) and used their overlapping markers (77 loci of the target exonic and flanking regions) to test the monophyly of Serianthes and to investigate generic relationships within the Archidendron clade using 55 ingoid plus two outgroup taxa. We show that Serianthes is monophyletic, confirm the Serianthes + Falcataria sister relationship to Wallaceodendron and recognise this combined clade as the Serianthes clade within the Archidendron clade. We also evaluated the use of overlapping loci across datasets in combination with concordance analyses to test generic relationships and further investigate previously unresolved relationships across the wider ingoid clade. Concordance analysis revealed limited gene tree conflicts near the tips of the Archidendron clade, but increased discordance at the base of the clade, which could be attributed to rapid lineage divergence (radiation) and/or incomplete lineage sorting.
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Affiliation(s)
- Else Demeulenaere
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Tom Schils
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - J. Gordon Burleigh
- Marine Laboratory, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Jens J. Ringelberg
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stefanie M. Ickert-Bond
- Evolutionary Biology & Ecology, Free University of Brussels, Av. F.D. Roosevelt, 50, CP 160/12 - B-1050 Brussels, Belgium
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Yahara T, Hirota SK, Fuse K, Sato H, Tagane S, Suyama Y. A new subspecies of Stellariaalsine (Caryophyllaceae) from Yakushima, Japan. PHYTOKEYS 2021; 187:177-188. [PMID: 35068974 PMCID: PMC8738627 DOI: 10.3897/phytokeys.187.64023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/24/2021] [Indexed: 06/14/2023]
Abstract
An unknown taxon of Stellaria was discovered in Yakushima, a Japanese island known to harbor several endemic species. To determine the identity of this taxon, this study employed MIG-seq for the reconstruction of a finely resolved phylogenetic tree of the newly discovered taxon, along with some related species of Stellaria. The results showed that the newly discovered taxon is a relative of S.alsine. Based on this result, Stellariaalsinesubsp.nanasubsp. nov. was published.
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Affiliation(s)
- Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityFukuokaJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
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Suyama Y, Hirota SK, Matsuo A, Tsunamoto Y, Mitsuyuki C, Shimura A, Okano K. Complementary combination of multiplex high‐throughput
DNA
sequencing for molecular phylogeny. Ecol Res 2021. [DOI: 10.1111/1440-1703.12270] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshihisa Suyama
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Shun K. Hirota
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Yoshihiro Tsunamoto
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Chika Mitsuyuki
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Atsuki Shimura
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
| | - Kunihiro Okano
- Department of Biological Environment Akita Prefectural University Akita Japan
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7
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Yahara T, Hirota SK, Fuse K, Sato H, Tagane S, Suyama Y. Validation of Hostaalata (Asparagaceae) as a new species and its phylogenetic affinity. PHYTOKEYS 2021; 181:79-93. [PMID: 34566449 PMCID: PMC8433123 DOI: 10.3897/phytokeys.181.64245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Molecular phylogenetic studies of Hostapulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H.pulchella to H.alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H.alata collections sympatric with H.pulchella, we find the two species closely related, but distinct. As such, we formally describe Hostaalata sp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.
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Affiliation(s)
- Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
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Cho MS, Takayama K, Yang J, Maki M, Kim SC. Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation. FRONTIERS IN PLANT SCIENCE 2021; 12:706195. [PMID: 34539700 PMCID: PMC8445234 DOI: 10.3389/fpls.2021.706195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
| | | | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Raimondeau P, Manzi S, Brucato N, Kinipi C, Leavesley M, Ricaut FX, Besnard G. Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity. Gene 2021; 800:145845. [PMID: 34274465 DOI: 10.1016/j.gene.2021.145845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.
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Affiliation(s)
- Pauline Raimondeau
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Sophie Manzi
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Christopher Kinipi
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea; CABAH & College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France.
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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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