1
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Hogg CJ, Edwards RJ, Farquharson KA, Silver LW, Brandies P, Peel E, Escalona M, Jaya FR, Thavornkanlapachai R, Batley K, Bradford TM, Chang JK, Chen Z, Deshpande N, Dziminski M, Ewart KM, Griffith OW, Marin Gual L, Moon KL, Travouillon KJ, Waters P, Whittington CM, Wilkins MR, Helgen KM, Lo N, Ho SYW, Ruiz Herrera A, Paltridge R, Marshall Graves JA, Renfree M, Shapiro B, Ottewell K, Belov K. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 2024; 8:1311-1326. [PMID: 38945974 PMCID: PMC11239497 DOI: 10.1038/s41559-024-02436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 07/02/2024]
Abstract
Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.
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Affiliation(s)
- Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Frederick R Jaya
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kimberley Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - J King Chang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Martin Dziminski
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Oliver W Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Laia Marin Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Paul Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Aurora Ruiz Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Rachel Paltridge
- Indigenous Desert Alliance, Alice Springs, Northern Territory, Australia
| | | | - Marilyn Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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2
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Crossman CA, Hamilton PK, Brown MW, Conger LA, George RC, Jackson KA, Radvan SN, Frasier TR. Effects of inbreeding on reproductive success in endangered North Atlantic right whales. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240490. [PMID: 39086821 PMCID: PMC11289666 DOI: 10.1098/rsos.240490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/24/2024] [Indexed: 08/02/2024]
Abstract
Only approximately 356 North Atlantic right whales (Eubalaena glacialis) remain. With extremely low levels of genetic diversity, limited options for mates, and variation in reproductive success across females, there is concern regarding the potential for genetic limitations of population growth from inbreeding depression. In this study, we quantified reproductive success of female North Atlantic right whales with a modified de-lifing approach using reproductive history information collected over decades of field observations. We used double-digest restriction site-associated sequencing to sequence approximately 2% of the genome of 105 female North Atlantic right whales and combined genomic inbreeding estimates with individual fecundity values to assess evidence of inbreeding depression. Inbreeding depression could not explain the variance in reproductive success of females, however we present evidence that inbreeding depression may be affecting the viability of inbred fetuses-potentially lowering the reproductive success of the species as a whole. Combined, these results allay some concerns that genetic factors are impacting species survival as genetic diversity is being retained through selection against inbred fetuses. While still far fewer calves are being born each year than expected, the small role of genetics underlying variance in female fecundity suggests that variance may be explained by external factors that can potentially be mitigated through protection measures designed to reduce serious injury and mortality from human activities.
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Affiliation(s)
- Carla A. Crossman
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Philip K. Hamilton
- Anderson Cabot Center for Ocean Life, New England Aquarium, Central Wharf, Boston, Massachusetts, USA
| | - Moira W. Brown
- Canadian Whale Institute, Welshpool, New Brunswick, Canada
| | - Lisa A. Conger
- NOAA Fisheries, Northeast Fisheries Science Center, Woods Hole, MA, USA
| | - R. Clay George
- Georgia Department of Natural Resources, Wildlife Conservation Section, Brunswick, GA, USA
| | - Katharine A. Jackson
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Saint Petersburg, FL, USA
| | - Sonya N. Radvan
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Timothy R. Frasier
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
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Hemstrom W, Grummer JA, Luikart G, Christie MR. Next-generation data filtering in the genomics era. Nat Rev Genet 2024:10.1038/s41576-024-00738-6. [PMID: 38877133 DOI: 10.1038/s41576-024-00738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering - removing sequencing bases, reads, genetic variants and/or individuals from a dataset - to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomic data filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy-Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima's D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne).
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Affiliation(s)
- William Hemstrom
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Jared A Grummer
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA.
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Peralta DM, Túnez JI, Rodríguez Cruz UE, Ceballos SG. A rapid approach for sex assignment by RAD-seq using a reference genome. PLoS One 2024; 19:e0297987. [PMID: 38578816 PMCID: PMC10997085 DOI: 10.1371/journal.pone.0297987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/14/2024] [Indexed: 04/07/2024] Open
Abstract
Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.
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Affiliation(s)
- Diego M. Peralta
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ecología de la Diversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Juan I. Túnez
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Ulises E. Rodríguez Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Santiago G. Ceballos
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
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Aguirre NC, Villalba PV, García MN, Filippi CV, Rivas JG, Martínez MC, Acuña CV, López AJ, López JA, Pathauer P, Palazzini D, Harrand L, Oberschelp J, Marcó MA, Cisneros EF, Carreras R, Martins Alves AM, Rodrigues JC, Hopp HE, Grattapaglia D, Cappa EP, Paniego NB, Marcucci Poltri SN. Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden). Front Genet 2024; 15:1361418. [PMID: 38606359 PMCID: PMC11008695 DOI: 10.3389/fgene.2024.1361418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/19/2024] [Indexed: 04/13/2024] Open
Abstract
Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.
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Affiliation(s)
| | | | - Martín Nahuel García
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Juan Gabriel Rivas
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - María Carolina Martínez
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Cintia Vanesa Acuña
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Augusto J. López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Juan Adolfo López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Pablo Pathauer
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Dino Palazzini
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Leonel Harrand
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Javier Oberschelp
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Martín Alberto Marcó
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Esteban Felipe Cisneros
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Rocío Carreras
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Ana Maria Martins Alves
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - José Carlos Rodrigues
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - H. Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Dario Grattapaglia
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Recursos Genéticos e Biotecnologia, Brasilia, Brazil
| | - Eduardo Pablo Cappa
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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Skorupski J, Brandes F, Seebass C, Festl W, Śmietana P, Balacco J, Jain N, Tilley T, Abueg L, Wood J, Sims Y, Formenti G, Fedrigo O, Jarvis ED. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. Int J Mol Sci 2023; 24:14816. [PMID: 37834264 PMCID: PMC10573602 DOI: 10.3390/ijms241914816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Florian Brandes
- Wildtier- und Artenschutzstation e.V., Hohe Warte 1, 31553 Sachsenhagen, Germany
| | | | - Wolfgang Festl
- EuroNerz e.V., Kleine Gildewart 3, 49074 Osnabrück, Germany
| | - Przemysław Śmietana
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Jonathan Wood
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Ying Sims
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
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7
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Martina M, Acquadro A, Portis E, Barchi L, Lanteri S. Diversity analyses in two ornamental and large-genome Ranunculaceae species based on a low-cost Klenow NGS-based protocol. FRONTIERS IN PLANT SCIENCE 2023; 14:1187205. [PMID: 37360724 PMCID: PMC10289064 DOI: 10.3389/fpls.2023.1187205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.
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8
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Atsawawaranunt K, Ewart KM, Major RE, Johnson RN, Santure AW, Whibley A. Tracing the introduction of the invasive common myna using population genomics. Heredity (Edinb) 2023:10.1038/s41437-023-00621-w. [PMID: 37193854 DOI: 10.1038/s41437-023-00621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.
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Affiliation(s)
| | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- National Museum of Natural History, Smithsonian Institution, Washington D.C., DC, USA
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Abeyrama DK, Boyle B, Burg TM. Comparison of genotyping by sequencing procedures to determine population genetic structure. Funct Integr Genomics 2022; 23:9. [PMID: 36538186 DOI: 10.1007/s10142-022-00929-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/07/2022] [Accepted: 11/16/2022] [Indexed: 03/21/2023]
Abstract
Advancements in technology over the past few decades have resulted in the development of genome sequencing at lower costs. Protocols, costs, and the amount of data produced by different sequencing technologies are highly variable. Ion Torrent and Illumina sequencing instruments are two sequencing technologies which use very similar library preparation procedures. Enzymatic combinations can be changed in genotyping by sequencing (GbS) library protocols without significant adjustments. To compare the outputs from two different GbS procedures, we sequenced samples of two sister species of yellow-nosed albatross collected at multiple geographic locations. The data sets involving different sequencing instruments and enzymatic combinations were analysed using the Stacks pipeline and aligned to the same reference genome. Both procedures identified the same genetic clusters separating Atlantic and Indian yellow-nosed albatross and substructure within Indian yellow-nosed albatross.
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10
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Chen Y, Zhang HL, Zhang L, Nizamani MM, Zhou T, Zhang H, Liu T. Genetic diversity assessment of Hopea hainanensis in Hainan Island. FRONTIERS IN PLANT SCIENCE 2022; 13:1075102. [PMID: 36570896 PMCID: PMC9767952 DOI: 10.3389/fpls.2022.1075102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Hopea hainanensis (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China, and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. The wood of Hopea hainanensis has a very high utilization value in nature since it is compact in structure, hard in texture, not easily deformed after drying, durable, and resistant to sunlight and water. As a result of its high quality, it has been felled and mined by humans without restraint, resulting in a reduction of its population size, severe habitat fragmentation, and a sharp decline in its population. Therefore, its conservation biology needs to be researched urgently. Researchers are currently focusing on the ecological factors and seed germination in the habitat of Hopea hainanensis to determine its endangered status. In the literature, there are no systematic analyses of the endangered mechanism of Hopea hainanensis in terms of genetic diversity. It focuses especially on the systematic genetic diversity of Hopea hainanensis in fragmented habitats. Using single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS) technology, 42 samples from seven different cohabitation groups were genotyped. The results showed that the average heterozygosity of the six populations of Hopea hainanensis was 19.77%, which indicated that the genetic diversity of Hopea hainanensis was low. Genetic diversity research is essential for rare and endangered plant protection research. We can find a scientific basis for protecting endangered plants on slope bases by analyzing genetic differences and relationships among populations.
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Affiliation(s)
- Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Hai-Li Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life Sciences, Hainan University, Haikou, China
| | - Li Zhang
- Guizhou Normal University Museum, Guizhou Normal University, Guizhou, China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, China
| | - Taoxiu Zhou
- College of Biological Science and Technology, Yangzhou University, Yangzhou, China
| | - Haiyang Zhang
- College of International Studies, Sichuan University, Chengdu, China
| | - Tingting Liu
- Guizhou Normal University Museum, Guizhou Normal University, Guizhou, China
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11
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Farquharson KA, McLennan EA, Cheng Y, Alexander L, Fox S, Lee AV, Belov K, Hogg CJ. Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program. iScience 2022; 25:104474. [PMID: 35754729 PMCID: PMC9218385 DOI: 10.1016/j.isci.2022.104474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/06/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species’ range (64,519 km2). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumor disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for “resistance” alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012 and 2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures. Developed target capture to assess functional diversity at over 500 genes Fine-scale structure exists in the genetically depauperate Tasmanian devil Insurance metapopulation is representative of wild genetic diversity Allele frequencies at disease-associated loci were similar in captivity to the wild
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Affiliation(s)
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Lauren Alexander
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, Tas 7001, Australia.,Toledo Zoo, 2605 Broadway, Toledo, OH 43609, USA
| | - Andrew V Lee
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, Tas 7001, Australia.,Toledo Zoo, 2605 Broadway, Toledo, OH 43609, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.,San Diego Zoo Wildlife Alliance, PO BOX 120551, San Diego, CA 92112, USA
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12
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Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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13
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Kolmer JA, Herman A, Fellers JP. Genotype Groups of the Wheat Leaf Rust Fungus Puccinia triticina in the United States as Determined by Genotyping by Sequencing. PHYTOPATHOLOGY 2022; 112:653-662. [PMID: 34261342 DOI: 10.1094/phyto-03-21-0125-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Wheat leaf rust caused by Puccinia triticina is a widespread disease of wheat in the United States and worldwide. Populations of P. triticina are characterized by virulence phenotypes that change rapidly because of selection by wheat cultivars with leaf rust resistance genes. The objective of this study was to genotype collections of P. triticina from 2011 to 2018 in the United States using restriction site-associated genotyping by sequencing (GBS) to determine if recently identified new virulence phenotypes belong to established genotype groups or to groups previously not detected. A total of 158 isolates were phenotyped for virulence on 20 lines of Thatcher wheat that are isogenic for leaf rust resistance genes and also genotyped for single nucleotide polymorphism. Eight distinct groups of P. triticina genotypes from common wheat were described based on coancestry, nucleotide divergence, and principal coordinate plots. A separate genotype group had isolates with virulence to durum wheat. Isolates within groups had similar virulence phenotypes, and the overall population had high levels of heterozygosity and high levels of linkage disequilibria, which were all indicators of clonality. Two new genotype groups were described, thereby raising the possibility of new introductions of P. triticina; however, genotypes in these groups may have also originated from somatic nuclear exchange and recombination. A genome-wide association study detected 19 single nucleotide polymorphisms that were highly associated with virulence to 11 resistance genes in the Thatcher near-isogenic lines.
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Affiliation(s)
- J A Kolmer
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108
| | - A Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - J P Fellers
- U.S. Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506
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14
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Babineau M, Collis E, Ruffell A, Bunch R, McNally J, Lyons RE, Kotze AC, Hunt PW. Selection of genome-wide SNPs for pooled allelotyping assays useful for population monitoring. Genome Biol Evol 2022; 14:6531970. [PMID: 35179579 PMCID: PMC8911822 DOI: 10.1093/gbe/evac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2022] [Indexed: 11/13/2022] Open
Abstract
Parasitic worms are serious pests of humans, livestock and crops worldwide. Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution. The evolution of chemical resistance, ecological changes, and pest dispersal have allowed an increasing number of pests to become difficult to control with current management methods. Their lifestyle limits the use of ecological and individual-based management of populations. There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies. This study presents a multi-locus, equal-representation, whole genome pooled SNPs selection approach as a monitoring tool for the ovine nematode parasite Haemonchus contortus. The SNP selection method used two reference genomes of different quality, then validated these SNPs against a high-quality recent genome assembly. From over 11 million high-quality SNPs identified, 334 SNPs were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools. As a proof-of-concept, 21 Australian H. contortus populations with various phenotypes and genotypes were screened. This analysis confirmed the overall low-level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance. The analysis showed that 66% of the SNPs were necessary for stability in assessing population genetic patterns, and SNP pairs did not show linkage according to allelic frequencies across the 21 populations. This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection. The SNP selection method could also be applied to other parasite species.
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Affiliation(s)
- M Babineau
- CSIRO Agriculture and Food, Armidale, Australia
| | - E Collis
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A Ruffell
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - R Bunch
- CSIRO Agriculture and Food, Armidale, Australia
| | - J McNally
- CSIRO Agriculture and Food, Armidale, Australia
| | - R E Lyons
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A C Kotze
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - P W Hunt
- CSIRO Agriculture and Food, Armidale, Australia
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15
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Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K. Threatened Species Initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci U S A 2022; 119:e2115643118. [PMID: 35042806 PMCID: PMC8795520 DOI: 10.1073/pnas.2115643118] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Kym Ottewell
- Conservation Science Centre, Department of Biodiversity, Conservation, & Attractions, Kensington, WA 6151, Australia
| | - Peter Latch
- Australian Government Department of Agriculture, Water & Environment, Canberra, ACT 2600, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - James Biggs
- Zoo and Aquarium Association Australasia, Mosman, NSW 2088, Australia
| | | | | | - Katherine Belov
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia
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16
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McLennan EA, Belov K, Hogg CJ, Grueber CE. How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02462. [PMID: 34614257 DOI: 10.1002/eap.2462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Conservation introductions to islands and fenced enclosures are increasing as in situ mitigations fail to keep pace with population declines. Few studies consider the potential loss of genetic diversity and increased inbreeding if released individuals breed disproportionately. As funding is limited and post-release monitoring expensive for conservation programs, understanding how sampling effort influences estimates of reproductive variance is useful. To investigate this relationship, we used a well-studied population of Tasmanian devils (Sarcophilus harrisii) introduced to Maria Island, Tasmania, Australia. Pedigree reconstruction based on molecular data revealed high variance in number of offspring per breeder and high proportions of unsuccessful individuals. Computational subsampling of 20%, 40%, 60%, and 80% of observed offspring resulted in inaccurate estimates of reproductive variance compared to the pedigree reconstructed with all sampled individuals. With decreased sampling effort, the proportion of inferred unsuccessful individuals was overestimated and the variance in number of offspring per breeder was underestimated. To accurately estimate reproductive variance, we recommend sampling as many individuals as logistically possible during the early stages of population establishment. Further, we recommend careful selection of colonizing individuals as they may be disproportionately represented in subsequent generations. Within the conservation management context, our results highlight important considerations for sample collection and post-release monitoring during population establishment.
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Affiliation(s)
- Elspeth A McLennan
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
- San Diego Zoo Global, PO BOX 120551, San Diego, California, 92112, USA
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17
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Tyagi SK, Mehrotra A, Singh A, Kumar A, Dutt T, Mishra BP, Pandey AK. Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India. Front Genet 2021; 12:673697. [PMID: 34737760 PMCID: PMC8560740 DOI: 10.3389/fgene.2021.673697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.
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Affiliation(s)
- Shiv K Tyagi
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Arnav Mehrotra
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Akansha Singh
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Amit Kumar
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu P Mishra
- Animal Biotechnology, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Ashwni K Pandey
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
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18
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Metapopulation management of a critically endangered marsupial in the age of genomics. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Development of SNP Set for the Marker-Assisted Selection of Guar ( Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. PLANTS 2021; 10:plants10102063. [PMID: 34685872 PMCID: PMC8539970 DOI: 10.3390/plants10102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022]
Abstract
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.
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20
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Samaha G, Wade CM, Mazrier H, Grueber CE, Haase B. Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management. BMC Genomics 2021; 22:601. [PMID: 34362297 PMCID: PMC8348863 DOI: 10.1186/s12864-021-07899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus). Results Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases. Conclusions The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07899-2.
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Affiliation(s)
- Georgina Samaha
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
| | - Claire M Wade
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Hamutal Mazrier
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Bianca Haase
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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21
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Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese. Genes (Basel) 2021; 12:genes12081203. [PMID: 34440377 PMCID: PMC8393582 DOI: 10.3390/genes12081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs' filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs-which had different allelic frequencies-were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.
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22
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Genomics for conservation: a case study of behavioral genes in the Tasmanian devil. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Sarfraz Z, Iqbal MS, Geng X, Iqbal MS, Nazir MF, Ahmed H, He S, Jia Y, Pan Z, Sun G, Ahmad S, Wang Q, Qin H, Liu J, Liu H, Yang J, Ma Z, Xu D, Yang J, Zhang J, Li Z, Cai Z, Zhang X, Zhang X, Huang A, Yi X, Zhou G, Li L, Zhu H, Pang B, Wang L, Sun J, Du X. GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton ( Gossypium hirsutum L.) Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:565552. [PMID: 34093598 PMCID: PMC8173050 DOI: 10.3389/fpls.2021.565552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.
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Affiliation(s)
- Zareen Sarfraz
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Shahid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Haris Ahmed
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, China
| | - Saghir Ahmad
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Qinglian Wang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Hongde Qin
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jinhai Liu
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Hui Liu
- Jing Hua Seed Industry Technologies Inc., Jingzhou, China
| | - Jun Yang
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Dongyong Xu
- Guoxin Rural Technical Service Association, Hebei, China
| | - Jinlong Yang
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Zhikun Li
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Zhongmin Cai
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Xin Zhang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Aifen Huang
- Sanyi Seed Industry of Changde in Hunan Inc., Changde, China
| | - Xianda Yi
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guanyin Zhou
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Lin Li
- Zhongli Company of Shandong, Shandong, China
| | - Haiyong Zhu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Baoyin Pang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
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Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
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25
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Casanova A, Maroso F, Blanco A, Hermida M, Ríos N, García G, Manuzzi A, Zane L, Verissimo A, García-Marín JL, Bouza C, Vera M, Martínez P. Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species. BMC Genomics 2021; 22:150. [PMID: 33653268 PMCID: PMC7927381 DOI: 10.1186/s12864-021-07465-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Background The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. Results Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. Conclusions Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07465-w.
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Affiliation(s)
- Adrián Casanova
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain.,Present address: Dipartimento di Scienze della Vita e Biotecnologia (SVeB), Università degli Studi di Ferrara, via Luigi Borsari, 46 - 44121, Ferrara, Italy
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain
| | - Néstor Ríos
- Sección Genética Evolutiva. Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Graciela García
- Sección Genética Evolutiva. Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Alice Manuzzi
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Lorenzo Zane
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy
| | - Ana Verissimo
- CIBIO - U.P. - Research Center for Biodiversity and Genetic Resources, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Virginia Institute of Marine Science, College of William and Mary, Route 1208, Greate Road, Gloucester Point, VA, 23062, USA
| | - José-Luís García-Marín
- Laboratori d'Ictiologia Genètica, Departamento de Biología, Faculty of Sciences, University of Girona, Campus of Montilivi, ES-17071, Girona, Spain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain. .,Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
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26
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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27
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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28
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Farquharson KA, Hogg CJ, Belov K, Grueber CE. Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs. Evol Appl 2020; 13:2179-2189. [PMID: 33005217 PMCID: PMC7513713 DOI: 10.1111/eva.12981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 02/19/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022] Open
Abstract
Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviors. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials; however, this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalized linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three nonmutually exclusive mate choice hypotheses: (a) advantage of heterozygous individuals, (b) advantage of dissimilar mates, and (c) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that nongenetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
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Affiliation(s)
- Katherine A Farquharson
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Katherine Belov
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
- San Diego Zoo Global San Diego USA
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29
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Genetic impacts of conservation management actions in a critically endangered parrot species. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01292-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA.,University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA.,Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA.,University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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31
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McLennan EA, Grueber CE, Wise P, Belov K, Hogg CJ. Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore. Anim Conserv 2020. [DOI: 10.1111/acv.12589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- E. A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
| | - P. Wise
- Save the Tasmanian Devil Program, DPIPWE Hobart Tas Australia
| | - K. Belov
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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32
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Armstrong EE, Taylor RW, Miller DE, Kaelin CB, Barsh GS, Hadly EA, Petrov D. Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biol 2020; 18:3. [PMID: 31915011 PMCID: PMC6950864 DOI: 10.1186/s12915-019-0734-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.
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Affiliation(s)
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA
- End2EndGenomics, LLC, Davis, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Seattle Children's Hospital and The University of Washington, Seattle, WA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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33
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Liu S, An Y, Tong W, Qin X, Samarina L, Guo R, Xia X, Wei C. Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research. BMC Genomics 2019; 20:935. [PMID: 31805860 PMCID: PMC6896268 DOI: 10.1186/s12864-019-6347-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.
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Affiliation(s)
- Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiuju Qin
- Guangxi LuYI Institute of Tea Tree Species, 17 Jinji Road, Guilin, China
| | - Lidia Samarina
- Department of Biotechnology, Russian Research Institute of Floriculture and Subtropical Crops, Sochi, Russia
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China.
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Brandies P, Peel E, Hogg CJ, Belov K. The Value of Reference Genomes in the Conservation of Threatened Species. Genes (Basel) 2019; 10:E846. [PMID: 31717707 PMCID: PMC6895880 DOI: 10.3390/genes10110846] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
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Affiliation(s)
| | | | | | - Katherine Belov
- School of Life & Environmental Sciences, The University of Sydney, Sydney 2006, Australia; (P.B.); (E.P.); (C.J.H.)
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