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Jones JM, Reinke SN, Mousavi-Derazmahalleh M, Garssen J, Jenmalm MC, Srinivasjois R, Silva D, Keelan J, Prescott SL, Palmer DJ, Christophersen CT. Maternal prebiotic supplementation during pregnancy and lactation modifies the microbiome and short chain fatty acid profile of both mother and infant. Clin Nutr 2024; 43:969-980. [PMID: 38452522 DOI: 10.1016/j.clnu.2024.02.030] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND & AIMS Improving maternal gut health in pregnancy and lactation is a potential strategy to improve immune and metabolic health in offspring and curtail the rising rates of inflammatory diseases linked to alterations in gut microbiota. Here, we investigate the effects of a maternal prebiotic supplement (galacto-oligosaccharides and fructo-oligosaccharides), ingested daily from <21 weeks' gestation to six months' post-partum, in a double-blinded, randomised placebo-controlled trial. METHODS Stool samples were collected at multiple timepoints from 74 mother-infant pairs as part of a larger, double-blinded, randomised controlled allergy intervention trial. The participants were randomised to one of two groups; with one group receiving 14.2 g per day of prebiotic powder (galacto-oligosaccharides GOS and fructo-oligosaccharides FOS in ratio 9:1), and the other receiving a placebo powder consisting of 8.7 g per day of maltodextrin. The faecal microbiota of both mother and infants were assessed based on the analysis of bacterial 16S rRNA gene (V4 region) sequences, and short chain fatty acid (SCFA) concentrations in stool. RESULTS Significant differences in the maternal microbiota profiles between baseline and either 28-weeks' or 36-weeks' gestation were found in the prebiotic supplemented women. Infant microbial beta-diversity also significantly differed between prebiotic and placebo groups at 12-months of age. Supplementation was associated with increased abundance of commensal Bifidobacteria in the maternal microbiota, and a reduction in the abundance of Negativicutes in both maternal and infant microbiota. There were also changes in SCFA concentrations with maternal prebiotics supplementation, including significant differences in acetic acid concentration between intervention and control groups from 20 to 28-weeks' gestation. CONCLUSION Maternal prebiotic supplementation of 14.2 g per day GOS/FOS was found to favourably modify both the maternal and the developing infant gut microbiome. These results build on our understanding of the importance of maternal diet during pregnancy, and indicate that it is possible to intervene and modify the development of the infant microbiome by dietary modulation of the maternal gut microbiome.
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Affiliation(s)
- Jacquelyn M Jones
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA 6027, Australia.
| | - Stacey N Reinke
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CS Utrecht, the Netherlands; Nutricia Research, 3584 CT Utrecht, the Netherlands
| | - Maria C Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Ravisha Srinivasjois
- Joondalup Health Campus, Joondalup, WA 6027, Australia; School of Medicine, The University of Western Australia, Crawley, WA 6009, Australia
| | - Desiree Silva
- Joondalup Health Campus, Joondalup, WA 6027, Australia; School of Medicine, The University of Western Australia, Crawley, WA 6009, Australia; Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia; School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Jeffrey Keelan
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia; School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Susan L Prescott
- School of Medicine, The University of Western Australia, Crawley, WA 6009, Australia; Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia; Department of Immunology and Dermatology, Perth Children's Hospital, Nedlands, WA 6009, Australia; Nova Institute for Health, Baltimore, MD 21231, USA
| | - Debra J Palmer
- School of Medicine, The University of Western Australia, Crawley, WA 6009, Australia; Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Claus T Christophersen
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA 6027, Australia; Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
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Lines R, Juggernauth M, Peverley G, Keating J, Simpson T, Mousavi-Derazmahalleh M, Bunce M, Berry TE, Taysom A, Bernardino AF, Whittle P. A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure. Mar Environ Res 2023; 192:106239. [PMID: 37926039 DOI: 10.1016/j.marenvres.2023.106239] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019; Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500 km of coastline. Metabarcoding assays targeting the mitochondrial genes 16S rRNA and COI were used to detect fish, marine mammals and elasmobranchs. We detected temporal differences between seasons and spatial differences between rivers/estuaries sampled. Overall, the largest eDNA survey in Brazil to date revealed 69 families from Class Actinopterygii (fish), 15 species from Class Chondrichthyes (sharks and rays), 4 species of marine and estuarine mammals and 23 species of conservation significance including 2 species of endangered dolphin. Our large-scale study reinforces the value eDNA metabarcoding can bring when monitoring the biodiversity of coastal environments and demonstrates the importance of collection of time-stamped environmental samples to better understand the impacts of anthropogenic activities.
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Affiliation(s)
- Rose Lines
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia.
| | | | - Georgia Peverley
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Tiffany Simpson
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Michael Bunce
- Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Tina E Berry
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Angelo F Bernardino
- Grupo de Ecologia Bentônica, Universidade Federal do Espirito Santo, Vitória, ES, Brazil
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Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. Sci Total Environ 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
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Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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4
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Jones J, Reinke SN, Mousavi-Derazmahalleh M, Palmer DJ, Christophersen CT. Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism. Front Microbiol 2022; 13:905901. [PMID: 35966698 PMCID: PMC9371947 DOI: 10.3389/fmicb.2022.905901] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
The human gut microbiome has increasingly been associated with autism spectrum disorder (ASD), which is a neurological developmental disorder, characterized by impairments to social interaction. The ability of the gut microbiota to signal across the gut-brain-microbiota axis with metabolites, including short-chain fatty acids, impacts brain health and has been identified to play a role in the gastrointestinal and developmental symptoms affecting autistic children. The fecal microbiome of older children with ASD has repeatedly shown particular shifts in the bacterial and fungal microbial community, which are significantly different from age-matched neurotypical controls, but it is still unclear whether these characteristic shifts are detectable before diagnosis. Early microbial colonization patterns can have long-lasting effects on human health, and pre-emptive intervention may be an important mediator to more severe autism. In this study, we characterized both the microbiome and short-chain fatty acid concentrations of fecal samples from young children between 21 and 40 months who were showing early behavioral signs of ASD. The fungal richness and acetic acid concentrations were observed to be higher with increasing autism severity, and the abundance of several bacterial taxa also changed due to the severity of ASD. Bacterial diversity and SCFA concentrations were also associated with stool form, and some bacterial families were found with differential abundance according to stool firmness. An exploratory analysis of the microbiome associated with pre-emptive treatment also showed significant differences at multiple taxonomic levels. These differences may impact the microbial signaling across the gut-brain-microbiota axis and the neurological development of the children.
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Affiliation(s)
- Jacquelyn Jones
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
- *Correspondence: Jacquelyn Jones
| | - Stacey N. Reinke
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
| | - Debra J. Palmer
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Claus T. Christophersen
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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5
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Rao WQ, Kalogeropoulos K, Allentoft ME, Gopalakrishnan S, Zhao WN, Workman CT, Knudsen C, Jiménez-Mena B, Seneci L, Mousavi-Derazmahalleh M, Jenkins TP, Rivera-de-Torre E, Liu SQ, Laustsen AH. The rise of genomics in snake venom research: recent advances and future perspectives. Gigascience 2022; 11:6562531. [PMID: 35365832 PMCID: PMC8975721 DOI: 10.1093/gigascience/giac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/14/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 12/12/2022] Open
Abstract
Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has matured rapidly over the past 2 decades, owing to the development of next-generation sequencing technologies, snake genomics remains in its infancy. Here, we provide an overview of the state of the art in snake genomics and discuss its potential implications for studying venom evolution and toxinology. On the basis of current knowledge, gene duplication and positive selection are key mechanisms in the neofunctionalization of snake venom proteins. This makes snake venoms important evolutionary drivers that explain the remarkable venom diversification and adaptive variation observed in these reptiles. Gene duplication and neofunctionalization have also generated a large number of repeat sequences in snake genomes that pose a significant challenge to DNA sequencing, resulting in the need for substantial computational resources and longer sequencing read length for high-quality genome assembly. Fortunately, owing to constantly improving sequencing technologies and computational tools, we are now able to explore the molecular mechanisms of snake venom evolution in unprecedented detail. Such novel insights have the potential to affect the design and development of antivenoms and possibly other drugs, as well as provide new fundamental knowledge on snake biology and evolution.
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Affiliation(s)
- Wei-Qiao Rao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark.,Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Konstantinos Kalogeropoulos
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia.,Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Wei-Ning Zhao
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Cecilie Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Belén Jiménez-Mena
- DTU Aqua, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Lorenzo Seneci
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Si-Qi Liu
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
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Gajdzik L, DeCarlo TM, Koziol A, Mousavi-Derazmahalleh M, Coghlan M, Power MW, Bunce M, Fairclough DV, Travers MJ, Moore GI, DiBattista JD. Climate-assisted persistence of tropical fish vagrants in temperate marine ecosystems. Commun Biol 2021; 4:1231. [PMID: 34711927 PMCID: PMC8553944 DOI: 10.1038/s42003-021-02733-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/01/2021] [Indexed: 11/08/2022] Open
Abstract
Rising temperatures and extreme climate events are propelling tropical species into temperate marine ecosystems, but not all species can persist. Here, we used the heatwave-driven expatriation of tropical Black Rabbitfish (Siganus fuscescens) to the temperate environments of Western Australia to assess the ecological and evolutionary mechanisms that may entail their persistence. Population genomic assays for this rabbitfish indicated little genetic differentiation between tropical residents and vagrants to temperate environments due to high migration rates, which were likely enhanced by the marine heatwave. DNA metabarcoding revealed a diverse diet for this species based on phytoplankton and algae, as well as an ability to feed on regional resources, including kelp. Irrespective of future climate scenarios, these macroalgae-consuming vagrants may self-recruit in temperate environments and further expand their geographic range by the year 2100. This expansion may compromise the health of the kelp forests that form Australia's Great Southern Reef. Overall, our study demonstrates that projected favourable climate conditions, continued large-scale genetic connectivity between populations, and diet versatility are key for tropical range-shifting fish to establish in temperate ecosystems.
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Affiliation(s)
- Laura Gajdzik
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Reef Ecology Laboratory, Red Sea Research Center, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia.
| | - Thomas M DeCarlo
- College of Natural and Computational Sciences, Hawai'i Pacific University, Honolulu, HI, 96744, USA
| | - Adam Koziol
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1017, Copenhagen, Denmark
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Megan Coghlan
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Matthew W Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
| | - David V Fairclough
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, 6920, Australia
| | - Michael J Travers
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, 6920, Australia
| | - Glenn I Moore
- Collections and Research, Western Australian Museum, Welshpool, WA, 6106, Australia
- School of Biological Sciences, University of Western Australia, Nedlands, WA, 6907, Australia
| | - Joseph D DiBattista
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, 2010, Australia
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Mousavi-Derazmahalleh M, Stott A, Lines R, Peverley G, Nester G, Simpson T, Zawierta M, De La Pierre M, Bunce M, Christophersen CT. eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity. Mol Ecol Resour 2021; 21:1697-1704. [PMID: 33580619 DOI: 10.1111/1755-0998.13356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way biodiversity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and noncurated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters. Finally, we present an in-house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an example of a published coral diversity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 samples. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data; scalability and reproducibility.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Audrey Stott
- Pawsey Supercomputing Centre, Kensington, WA, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Georgia Peverley
- eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michal Zawierta
- Department of Electrical, Electronic and Computer Engineering, The University of Western Australia, Nedlands, WA, Australia
| | | | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Environmental Protection Authority, Wellington, New Zealand
| | - Claus T Christophersen
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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Saccò M, Blyth AJ, Humphreys WF, Cooper SJB, White NE, Campbell M, Mousavi-Derazmahalleh M, Hua Q, Mazumder D, Smith C, Griebler C, Grice K. Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem. Sci Rep 2021; 11:3694. [PMID: 33580159 PMCID: PMC7881013 DOI: 10.1038/s41598-021-83286-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022] Open
Abstract
Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR—low rainfall and HR—high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.
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Affiliation(s)
- Mattia Saccò
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, 6102, Australia. .,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.
| | - Alison J Blyth
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, 6102, Australia.,School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - William F Humphreys
- Collections and Research Centre, Western Australian Museum, Welshpool, WA, 6986, Australia.,School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.,Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Matthew Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Colin Smith
- Department of Archaeology and History, La Trobe University, Bundoora, VIC, 3086, Australia.,Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1090, Vienna, Austria
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, 6102, Australia
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9
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Mousavi-Derazmahalleh M, Chang S, Thomas G, Derbyshire M, Bayer PE, Edwards D, Nelson MN, Erskine W, Lopez-Ruiz FJ, Clements J, Hane JK. Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics. BMC Genomics 2019; 20:385. [PMID: 31101009 PMCID: PMC6525431 DOI: 10.1186/s12864-019-5774-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/25/2018] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Background Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts. Results Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents. Conclusions Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Geoff Thomas
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Mark Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Phillip E Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Matthew N Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.,Current address: Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, 6913, Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Jon Clements
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia. .,Curtin Institute for Computation, Curtin University, Bentley, WA, 6102, Australia.
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10
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Derbyshire MC, Denton-Giles M, Hane JK, Chang S, Mousavi-Derazmahalleh M, Raffaele S, Buchwaldt L, Kamphuis LG. A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum. PLoS One 2019; 14:e0214201. [PMID: 30921376 PMCID: PMC6438532 DOI: 10.1371/journal.pone.0214201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/10/2019] [Indexed: 01/08/2023] Open
Abstract
The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.
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Affiliation(s)
- Mark Charles Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- * E-mail:
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Micro-organismes (LIPM), Université de Toulouse, INRA, Toulouse, France
| | - Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatchewan, Saskatoon, Canada
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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11
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Mousavi-Derazmahalleh M, Nevado B, Bayer PE, Filatov DA, Hane JK, Edwards D, Erskine W, Nelson MN. The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin. Theor Appl Genet 2018; 131:2543-2554. [PMID: 30225643 PMCID: PMC6244526 DOI: 10.1007/s00122-018-3171-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/25/2018] [Indexed: 05/21/2023]
Abstract
This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication. The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today's crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - James K Hane
- CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Matthew N Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.
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12
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Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. Theor Appl Genet 2018; 131:887-901. [PMID: 29353413 PMCID: PMC5852200 DOI: 10.1007/s00122-017-3045-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East-West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables. Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Bhavna Hurgobin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | | | - Lars G. Kamphuis
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Jens D. Berger
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - James K. Hane
- CCDM Bioinformatics, Centre for Crop Disease Management, Curtin University, Bentley, WA 6102 Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Matthew N. Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
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