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Gempo N, Yeshi K, Crayn D, Wangchuk P. Climate-Affected Australian Tropical Montane Cloud Forest Plants: Metabolomic Profiles, Isolated Phytochemicals, and Bioactivities. Plants (Basel) 2024; 13:1024. [PMID: 38611553 PMCID: PMC11013060 DOI: 10.3390/plants13071024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
The Australian Wet Tropics World Heritage Area (WTWHA) in northeast Queensland is home to approximately 18 percent of the nation's total vascular plant species. Over the past century, human activity and industrial development have caused global climate changes, posing a severe and irreversible danger to the entire land-based ecosystem, and the WTWHA is no exception. The current average annual temperature of WTWHA in northeast Queensland is 24 °C. However, in the coming years (by 2030), the average annual temperature increase is estimated to be between 0.5 and 1.4 °C compared to the climate observed between 1986 and 2005. Looking further ahead to 2070, the anticipated temperature rise is projected to be between 1.0 and 3.2 °C, with the exact range depending on future emissions. We identified 84 plant species, endemic to tropical montane cloud forests (TMCF) within the WTWHA, which are already experiencing climate change threats. Some of these plants are used in herbal medicines. This study comprehensively reviewed the metabolomics studies conducted on these 84 plant species until now toward understanding their physiological and metabolomics responses to global climate change. This review also discusses the following: (i) recent developments in plant metabolomics studies that can be applied to study and better understand the interactions of wet tropics plants with climatic stress, (ii) medicinal plants and isolated phytochemicals with structural diversity, and (iii) reported biological activities of crude extracts and isolated compounds.
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Affiliation(s)
- Ngawang Gempo
- Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia; (N.G.); (P.W.)
- College of Public Health, Medical and Veterinary Services (CPHMVS), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia
| | - Karma Yeshi
- Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia; (N.G.); (P.W.)
- College of Public Health, Medical and Veterinary Services (CPHMVS), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia
| | - Darren Crayn
- Australian Tropical Herbarium (ATH), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia;
| | - Phurpa Wangchuk
- Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia; (N.G.); (P.W.)
- College of Public Health, Medical and Veterinary Services (CPHMVS), James Cook University, Nguma-bada Campus, McGregor Rd., Cairns, QLD 4878, Australia
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Yeshi K, Ruscher R, Miles K, Crayn D, Liddell M, Wangchuk P. Antioxidant and Anti-Inflammatory Activities of Endemic Plants of the Australian Wet Tropics. Plants 2022; 11:plants11192519. [PMID: 36235388 PMCID: PMC9571949 DOI: 10.3390/plants11192519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/03/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
Plants have been a vital source of natural antioxidants since ancient times. Plants growing under various abiotic stress conditions often produce more defensive secondary metabolites such as phenolics, flavonoids, and terpenoids during adaptation to the environment. Many of these secondary metabolites are known to possess antioxidant and anti-inflammatory properties. This study tested seven plants sourced from the mountaintop areas (above 1000 m elevation) of Mount Lewis National Park (falls under the Wet Tropics of Queensland), Australia, for their antioxidant and anti-inflammatory activities. Of the seven studied plants, hydroethanolic extracts of six plants (Leptospermum wooroonooran, Ceratopetalum hylandii, Linospadix apetiolatus, Garcinia brassii, Litsea granitica, and Polyscias willmottii) showed high 2,2-diphenyl-1-picrylhydrazyl (DPPH)-free radical scavenging activity in a dose-dependent (25–1000 μg/mL) manner. At the highest concentration of 1 mg/mL, the DPPH free radical scavenged percentage varied between 75.4% and 92.3%. Only the species Alyxia orophila was inactive in the DPPH free radical scavenging assay. Pseudo-IC50 values of the extracts’ ferric reducing antioxidant power (FRAP) based on dose-response curves showed a significant positive correlation with total phenolic content. Five out of the seven plants, namely G. brassii, C. hylandii, L. apetiolatus, L. wooroonooran, and A. orophila, showed inhibitory effects on the secretion of proinflammatory cytokines, tumour necrosis factor (TNF), and interleukins (IL)-23 in a lipopolysaccharide (LPS)-stimulated human peripheral blood mononuclear cells (PBMCs) assay. The results of this study demonstrate the value of tropical mountaintop plants in the biodiscovery of antioxidant and anti-inflammatory lead compounds.
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Affiliation(s)
- Karma Yeshi
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4 and E5, McGregor Rd, Smithfield, QLD 4878, Australia
- Correspondence: (K.Y.); (P.W.)
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4 and E5, McGregor Rd, Smithfield, QLD 4878, Australia
| | - Kim Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4 and E5, McGregor Rd, Smithfield, QLD 4878, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Building E2, McGregor Rd, Smithfield, QLD 4878, Australia
| | - Michael Liddell
- College of Science and Engineering, Centre for Tropical Environmental and Sustainability Science, Building E1, McGregor Rd, Smithfield, QLD 4878, Australia
| | - Phurpa Wangchuk
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4 and E5, McGregor Rd, Smithfield, QLD 4878, Australia
- Correspondence: (K.Y.); (P.W.)
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Turpin G, Ritmejerytė E, Jamie J, Crayn D, Wangchuk P. Aboriginal medicinal plants of Queensland: ethnopharmacological uses, species diversity, and biodiscovery pathways. J Ethnobiol Ethnomed 2022; 18:54. [PMID: 35948982 PMCID: PMC9364609 DOI: 10.1186/s13002-022-00552-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Aboriginal peoples have occupied the island continent of Australia for millennia. Over 500 different clan groups or nations with distinctive cultures, beliefs, and languages have learnt to live sustainably and harmoniously with nature. They have developed an intimate and profound relationship with the environment, and their use of native plants in food and medicine is largely determined by the environment they lived in. Over 1511 plant species have been recorded as having been used medicinally in Australia. Most of these medicinal plants were recorded from the Aboriginal communities in Northern Territory, New South Wales, South Australia, and Western Australia. Not much has yet been reported on Aboriginal medicinal plants of Queensland. Therefore, the main aim of this review is to collect the literature on the medicinal plants used by Aboriginal peoples of Queensland and critically assess their ethnopharmacological uses. METHODS The information used in this review was collected from archival material and uploaded into the Tropical Indigenous Ethnobotany Centre (TIEC) database. Archival material included botanist's journals/books and old hard copy books. Scientific names of the medicinal plant species were matched against the 'World Flora Online Plant List', and 'Australian Plant Census' for currently accepted species names to avoid repetition. An oral traditional medical knowledge obtained through interviewing traditional knowledge holders (entered in the TIEC database) has not been captured in this review to protect their knowledge. RESULTS This review identified 135 species of Queensland Aboriginal medicinal plants, which belong to 103 genera from 53 families, with Myrtaceae being the highest represented plant family. While trees represented the biggest habit, leaves were the most commonly used plant parts. Of 62 different diseases treated by the medicinal plants, highest number of plants are used for treating skin sores and infections. Few plants identified through this review can be found in other tropical countries but many of these medicinal plants are native to Australia. Many of these medicinal plants are also used as bush food by Aboriginal peoples. CONCLUSION Through extensive literature review, we found that 135 medicinal plants native to Queensland are used for treating 62 different diseases, especially skin infections. Since these medicinal plants are also used as bush food and are rarely studied using the Western scientific protocols, there is a huge potential for bioprospecting and bush food industry.
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Affiliation(s)
- Gerry Turpin
- Tropical Indigenous Ethnobotany Centre, Australian Tropical Herbarium, James Cook University, Building E1, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia.
- Queensland Herbarium, Department of Environment and Science, Mount Coot-tha Botanical Gardens, Mount Coot-tha Road, Toowong, QLD, 4066, Australia.
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Edita Ritmejerytė
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia
| | - Joanne Jamie
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Building E1, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia
- Centre for Tropical Environmental Sustainability Science, James Cook University, PO Box 6811, Cairns, QLD, 4870, Australia
| | - Phurpa Wangchuk
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia.
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Bloesch Z, Nauheimer L, Elias Almeida T, Crayn D, Raymond Field A. HybPhaser identifies hybrid evolution in Australian Thelypteridaceae. Mol Phylogenet Evol 2022; 173:107526. [DOI: 10.1016/j.ympev.2022.107526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets. Appl Plant Sci 2021; 9:APS311441. [PMID: 34336402 PMCID: PMC8312746 DOI: 10.1002/aps3.11441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 05/24/2023]
Abstract
PREMISE Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.
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Affiliation(s)
- Lars Nauheimer
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Nicholas Weigner
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Elizabeth Joyce
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Charles Clarke
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Cairns Botanic GardensCollins AvenueEdge HillQueensland4870Australia
| | - Katharina Nargar
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- National Research Collections AustraliaCommonwealth Industrial and Scientific Research Organisation (CSIRO)GPO Box 1700CanberraAustralian Capital Territory2601Australia
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Yudina SV, Schelkunov MI, Nauheimer L, Crayn D, Chantanaorrapint S, Hroneš M, Sochor M, Dančák M, Mar SS, Luu HT, Nuraliev MS, Logacheva MD. Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction. Front Plant Sci 2021; 12:602598. [PMID: 33796122 PMCID: PMC8009136 DOI: 10.3389/fpls.2021.602598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/22/2021] [Indexed: 05/14/2023]
Abstract
Heterotrophic plants provide intriguing examples of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described; however, little is known about the latest stages of plastome reduction. Here we analyze a diversity of plastid genomes in a set of closely related non-photosynthetic plants. We demonstrate how a gradual loss of genes shapes the miniaturized plastomes of these plants. The subject of our study, the genus Thismia, represents the mycoheterotrophic monocot family Thismiaceae, a group that may have experienced a very ancient (60-80 mya) transition to heterotrophy. In all 18 species examined, the plastome is reduced to 14-18 kb and is highly AT-biased. The most complete observed gene set includes accD, seven ribosomal protein genes, three rRNA, and two tRNA genes. Different clades of Thismia have undergone further gene loss (complete absence or pseudogenization) compared to this set: in particular, we report two independent losses of rps2 and rps18.
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Affiliation(s)
- Sophia V. Yudina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Sahut Chantanaorrapint
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Michal Hroneš
- Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Olomouc, Czechia
| | - Martin Dančák
- Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | | | - Hong Truong Luu
- Southern Institute of Ecology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Maxim S. Nuraliev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
| | - Maria D. Logacheva
- Institute for Information Transmission Problems, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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Fisher MF, Payne CD, Chetty T, Crayn D, Berkowitz O, Whelan J, Rosengren KJ, Mylne JS. The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides. J Biol Chem 2020; 295:14510-14521. [PMID: 32817170 PMCID: PMC7573267 DOI: 10.1074/jbc.ra120.014781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/11/2020] [Indexed: 01/03/2023] Open
Abstract
Cyclic peptides are reported to have antibacterial, antifungal, and other bioactivities. Orbitides are a class of cyclic peptides that are small, head-to-tail cyclized, composed of proteinogenic amino acids and lack disulfide bonds; they are also known in several genera of the plant family Rutaceae. Melicope xanthoxyloides is the Australian rain forest tree of the Rutaceae family in which evolidine, the first plant cyclic peptide, was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, so to redress this we used tandem MS and de novo transcriptomics to rediscover evolidine and decipher its biosynthetic origin from a short precursor just 48 residues in length. We also identified another six M. xanthoxyloides orbitides using the same techniques. These peptides have atypically diverse C termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides, suggesting new cyclizing enzymes await discovery. We examined the structure of two of the novel orbitides by NMR, finding one had a definable structure, whereas the other did not. Mining RNA-seq and whole genome sequencing data from other species of the Rutaceae family revealed that a large and diverse family of peptides is encoded by similar sequences across the family and demonstrates how powerful de novo transcriptomics can be at accelerating the discovery of new peptide families.
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Affiliation(s)
- Mark F Fisher
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Colton D Payne
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Thaveshini Chetty
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - K Johan Rosengren
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
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Moner AM, Furtado A, Chivers I, Fox G, Crayn D, Henry RJ. Diversity and evolution of rice progenitors in Australia. Ecol Evol 2018; 8:4360-4366. [PMID: 29721304 PMCID: PMC5916314 DOI: 10.1002/ece3.3989] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/22/2018] [Accepted: 02/09/2018] [Indexed: 01/19/2023] Open
Abstract
In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest-branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon-like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.
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Affiliation(s)
- Ali M Moner
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Ian Chivers
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Darren Crayn
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
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Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnol J 2017; 15:765-774. [PMID: 27889940 PMCID: PMC5425390 DOI: 10.1111/pbi.12674] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 05/04/2023]
Abstract
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityCairnsQLDAustralia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandToowoombaQLDAustralia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
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Laity T, Laffan SW, González-Orozco CE, Faith DP, Rosauer DF, Byrne M, Miller JT, Crayn D, Costion C, Moritz CC, Newport K. Phylodiversity to inform conservation policy: An Australian example. Sci Total Environ 2015; 534:131-143. [PMID: 25976346 DOI: 10.1016/j.scitotenv.2015.04.113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 06/04/2023]
Abstract
Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone. The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation can include important elements of biodiversity in conservation planning, such as evolutionary potential and feature diversity that will improve decision-making and lead to better biodiversity conservation outcomes.
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Affiliation(s)
- Tania Laity
- Science Division, Department of Environment, GPO Box 787, Canberra, ACT 2601, Australia
| | - Shawn W Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Science, University of New South Wales, Sydney 2052, Australia
| | - Carlos E González-Orozco
- Institute for Applied Ecology and Collaborative Research for Murray-Darling Basin Futures, University of Canberra, Canberra, ACT 2601, Australia
| | - Daniel P Faith
- The Australian Museum Research Institute, Australian Museum, 6 College St, Sydney, NSW 2000, Australia
| | - Dan F Rosauer
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, ACT 2601, Australia; Centre for Biodiversity Analysis, The Australian National University, ACT 2601, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| | - Joseph T Miller
- Centre for Australian National Biodiversity Research, CSIRO, GPO Box 1600, Canberra, ACT, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns Campus, PO Box 6811, Smithfield, QLD 4878, Australia; Centre for Tropical Environmental Sustainability Science, James Cook University, Cairns Campus, PO Box 6811, Smithfield, QLD 4878, Australia
| | - Craig Costion
- Centre for Tropical Environmental Sustainability Science, James Cook University, Cairns Campus, PO Box 6811, Smithfield, QLD 4878, Australia; Botany Department, National Museum of Natural History, MRC 166, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Craig C Moritz
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, ACT 2601, Australia; Centre for Biodiversity Analysis, The Australian National University, ACT 2601, Australia
| | - Karl Newport
- Science Division, Department of Environment, GPO Box 787, Canberra, ACT 2601, Australia
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Holzmeyer L, Duretto M, Crayn D, Hörandl E, Heslewood M, Jayanthan J, Appelhans MS. Phylogeny of Acronychia (Rutaceae) and First Insights into Its Historical Biogeography and the Evolution of Fruit Characters. PLoS One 2015; 10:e0136296. [PMID: 26301574 PMCID: PMC4547736 DOI: 10.1371/journal.pone.0136296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Background The genus Acronychia (Citrus family, Rutaceae) contains 49 species of trees and shrubs that are found mainly in rain forest. The genus has a large distributional range from mainland southern Asia to Australia and New Caledonia, but most species are endemic to either New Guinea or Australia. This study aimed to provide the first detailed molecular phylogeny of Acronychia and use it to test the taxonomic value of fruit morphological characters, and infer the historical biogeography of the genus. Methodology Phylogenetic analyses (Bayesian Inference, Maximum Likelihood) were undertaken on nucleotide sequence data from two plastid (psbA-trnH, trnL-trnF) and three nuclear markers (ETS, ITS, NIAi3) from 29 Acronychia species (59% of the genus) and representatives of related genera. Results and Conclusions The results indicate that the South-East Asian genus Maclurodendron is nested phylogenetically within Acronychia and must be synonymized to render Acronychia monophyletic. Fruit morphological characters have been used previously to infer relationships within Acronychia and our analyses show that these characters are informative for some subclades but are homoplasious for the group as a whole. Apocarpous fruits are the ancestral state in Acronychia and subapocarpous and fully syncarpous fruits are derived. The unisexual flowers of Maclurodendron are derived from bisexual flowers, which are found in all species of Acronychia as well as its relatives. Acronychia probably first evolved on Australia with range expansion to New Guinea via stepping-stone dispersal or direct land connections within the Sahul Shelf, followed by two independent dispersals to areas west of New Guinea. Most species of Acronychia occur in either Australia or New Guinea, but no species occurs in both regions. This is surprising given the close proximity of the landmasses, but might be explained by ecological factors.
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Affiliation(s)
- Laura Holzmeyer
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Untere Karspüle 2, Göttingen, Germany
| | - Marco Duretto
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Australia
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Untere Karspüle 2, Göttingen, Germany
| | - Margaret Heslewood
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - Janani Jayanthan
- Australian Tropical Herbarium, James Cook University, Cairns, Australia
| | - Marc S. Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Untere Karspüle 2, Göttingen, Germany
- Department of Botany, Smithsonian Institution, Washington, DC, United States of America
- * E-mail:
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12
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Kooyman RM, Wilf P, Barreda VD, Carpenter RJ, Jordan GJ, Sniderman JMK, Allen A, Brodribb TJ, Crayn D, Feild TS, Laffan SW, Lusk CH, Rossetto M, Weston PH. Paleo-Antarctic rainforest into the modern Old World tropics: the rich past and threatened future of the "southern wet forest survivors". Am J Bot 2014; 101:2121-2135. [PMID: 25480709 DOI: 10.3732/ajb.1400340] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF STUDY Have Gondwanan rainforest floral associations survived? Where do they occur today? Have they survived continuously in particular locations? How significant is their living floristic signal? We revisit these classic questions in light of significant recent increases in relevant paleobotanical data.• METHODS We traced the extinction and persistence of lineages and associations through the past across four now separated regions-Australia, New Zealand, Patagonia, and Antarctica-using fossil occurrence data from 63 well-dated Gondwanan rainforest sites and 396 constituent taxa. Fossil sites were allocated to four age groups: Cretaceous, Paleocene-Eocene, Neogene plus Oligocene, and Pleistocene. We compared the modern and ancient distributions of lineages represented in the fossil record to see if dissimilarity increased with time. We quantified similarity-dissimilarity of composition and taxonomic structure among fossil assemblages, and between fossil and modern assemblages.• KEY RESULTS Strong similarities between ancient Patagonia and Australia confirmed shared Gondwanan rainforest history, but more of the lineages persisted in Australia. Samples of ancient Australia grouped with the extant floras of Australia, New Guinea, New Caledonia, Fiji, and Mt. Kinabalu. Decreasing similarity through time among the regional floras of Antarctica, Patagonia, New Zealand, and southern Australia reflects multiple extinction events.• CONCLUSIONS Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics.
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Affiliation(s)
- Robert M Kooyman
- Department of Biological Sciences, Macquarie University, North Ryde 2113, Sydney, Australia National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Viviana D Barreda
- Museo Argentino de Ciencias Naturales, CONICET, División Paleobotánica, Av. Ángel Gallardo 470, C1405DJR Buenos Aires, Argentina
| | - Raymond J Carpenter
- School of Earth and Environmental Sciences, Benham Bldg DX 650 312, University of Adelaide, South Australia, Australia
| | - Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, 7001 Tasmania, Australia
| | - J M Kale Sniderman
- School of Earth Sciences, University of Melbourne, Melbourne 3010, Australia
| | - Andrew Allen
- Department of Biological Sciences, Macquarie University, North Ryde 2113, Sydney, Australia
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, 7001 Tasmania, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, School of Marine and Tropical Biology, James Cook University, Cairns, Australia
| | - Taylor S Feild
- Australian Tropical Herbarium, School of Marine and Tropical Biology, James Cook University, Cairns, Australia
| | - Shawn W Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052, Sydney, Australia
| | - Christopher H Lusk
- School of Science, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Maurizio Rossetto
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
| | - Peter H Weston
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
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13
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Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ. Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia. Trop Plant Biol 2014; 7:111-120. [PMID: 25485030 PMCID: PMC4245483 DOI: 10.1007/s12042-014-9142-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/13/2014] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa L.) was probably domesticated from O. rufipogon in Asia in the last 10,000 years. Relatives of cultivated rice (A genome species of Oryza) are found in South America, Africa, Australia and Asia. These A genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. Members of this group in Northern Australia include, an annual species, O. meridionalis, and two recently distinguished perennial taxa, to one of which the name O. rufipogon has been applied and the other a perennial form of O. meridionalis. Comparison of whole chloroplast genome sequences of these taxa has now been used to determine the relationships between the wild taxa and cultivated rice. The chloroplast genomes of the perennials were both found to be distinguished from O. rufipogon from Asia by 124 or 125 variations and were distinguished from each other by 53 variations. These populations have remained isolated from the overwhelming genetic impact of the large domesticated rice populations in Asia and may be unique descendants of the gene pool from which domesticated rice arose. The conservation of this wild genetic resource may be critical for global food security.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ernnie Syafika Omar
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Australia
| | - Bryan Simon
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori Japan
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
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14
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Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, Flowers JM, Purugganan MD, Nakamura I, Sato YI, Sato T, Crayn D, Simon B, Waters DLE, Henry RJ, Ishikawa R. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. Rice (N Y) 2013; 6:26. [PMID: 24280095 PMCID: PMC3874672 DOI: 10.1186/1939-8433-6-26] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/09/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. RESULTS Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets. CONCLUSION Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.
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Affiliation(s)
- Masahiro Sotowa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuu Kobayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yin Hao
- Science of Cryobiosystem, The United Graduate School of Agriculture Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Katsunori Tanaka
- Faculty of Humanities, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Jonathan M Flowers
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 0271-8510, Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature, Kyoto 603-8047, Japan
| | - Tadashi Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland 6811, Australia
| | - Bryan Simon
- Queensland Herbarium, Brisbane Botanic Gardens Mt Coot-tha, Brisbane, Queensland 4066, Australia
| | - Daniel LE Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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15
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Costion C, Ford A, Cross H, Crayn D, Harrington M, Lowe A. Plant DNA barcodes can accurately estimate species richness in poorly known floras. PLoS One 2011; 6:e26841. [PMID: 22096501 PMCID: PMC3214028 DOI: 10.1371/journal.pone.0026841] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/04/2011] [Indexed: 11/19/2022] Open
Abstract
Background Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. Methodology/Principal Findings Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. Conclusions/Significance We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.
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Affiliation(s)
- Craig Costion
- Australian Centre for Ecology and Evolutionary Biology, University of Adelaide, Adelaide, South Australia, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
- * E-mail: (CC); (AL)
| | - Andrew Ford
- CSIRO Ecosystem Sciences, Tropical Forest Research Centre, Atherton, Queensland, Australia
| | - Hugh Cross
- Australian Centre for Ecology and Evolutionary Biology, University of Adelaide, Adelaide, South Australia, Australia
- State Herbarium of South Australia, Department for Environment and Natural Resources, Adelaide, South Australia, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
| | - Mark Harrington
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
| | - Andrew Lowe
- Australian Centre for Ecology and Evolutionary Biology, University of Adelaide, Adelaide, South Australia, Australia
- State Herbarium of South Australia, Department for Environment and Natural Resources, Adelaide, South Australia, Australia
- * E-mail: (CC); (AL)
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