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Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023; 55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
Abstract
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Graham M Hughes
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Colleen Lawless
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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2
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Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains. Sci Rep 2021; 11:17984. [PMID: 34504218 PMCID: PMC8429547 DOI: 10.1038/s41598-021-97401-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022] Open
Abstract
Habitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056-0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.
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3
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Bredemeyer KR, Harris AJ, Li G, Zhao L, Foley NM, Roelke-Parker M, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis). J Hered 2021; 112:165-173. [PMID: 33305796 PMCID: PMC8006817 DOI: 10.1093/jhered/esaa057] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022] Open
Abstract
In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Melody Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity-Center for Computer Technologies, ITMO University, Saint Petersburg, Russian Federation.,Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Wesley C Warren
- Bond Life Science Center, University of Missouri, Columbia, MO
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
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4
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Li G, Figueiró HV, Eizirik E, Murphy WJ. Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species. Mol Biol Evol 2020; 36:2111-2126. [PMID: 31198971 PMCID: PMC6759079 DOI: 10.1093/molbev/msz139] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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Affiliation(s)
- Gang Li
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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5
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Tensen L, Drouilly M, van Vuuren BJ. Genetic structure and diversity within lethally managed populations of two mesopredators in South Africa. J Mammal 2018. [DOI: 10.1093/jmammal/gyy127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Laura Tensen
- The Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park Campus, South Africa
| | - Marine Drouilly
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Upper Campus, Rondebosch, South Africa
| | - Bettine Jansen van Vuuren
- The Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park Campus, South Africa
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6
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Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Ginns EI, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton GD, Warren WC, Wasim M, Lyons LA. Applications and efficiencies of the first cat 63K DNA array. Sci Rep 2018; 8:7024. [PMID: 29728693 PMCID: PMC5935720 DOI: 10.1038/s41598-018-25438-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/16/2018] [Indexed: 12/02/2022] Open
Abstract
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
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Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Safat, Kuwait.
| | - Mona Abdi
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Leslie H Bach
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,University of San Francisco, San Francisco, CA, USA
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Nicholas H Dodman
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Edward I Ginns
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer C Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bianca Haase
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Jens Haggstrom
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michael J Hamilton
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Biochemistry, University of California - Riverside, Riverside, CA, USA
| | | | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Foothill College, Los Altos Hills, CA, USA
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, and The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Richard Malik
- Centre for Veterinary Education, University of Sydney, New South Wales, Australia
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael J Montague
- Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Carlyn B Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Clare Rusbridge
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Rashid Saif
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - G Diane Shelton
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Muhammad Wasim
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA.
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7
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Tensen L, Groom RJ, Khuzwayo J, Jansen van Vuuren B. The genetic tale of a recovering lion population (Panthera leo) in the Savé Valley region (Zimbabwe): A better understanding of the history and managing the future. PLoS One 2018; 13:e0190369. [PMID: 29415031 PMCID: PMC5802433 DOI: 10.1371/journal.pone.0190369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/13/2017] [Indexed: 11/24/2022] Open
Abstract
The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations.
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Affiliation(s)
- Laura Tensen
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Rosemary J. Groom
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
- African Wildlife Conservation Fund, Chishakwe Ranch, Savé Valley Conservancy, Zimbabwe
| | - Joy Khuzwayo
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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8
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Schmidt-Küntzel A, Dalton DL, Menotti-Raymond M, Fabiano E, Charruau P, Johnson WE, Sommer S, Marker L, Kotzé A, O’Brien SJ. Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation. CHEETAHS: BIOLOGY AND CONSERVATION 2018. [PMCID: PMC7149701 DOI: 10.1016/b978-0-12-804088-1.00006-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
From allozymes in 1983 to whole genomes in 2015, genetic studies of the cheetah have been extensive. In this chapter we provide an overview of the available literature. Overall, patterns of genetic variation provided evidence of low variability and suggest this loss occurred thousands of years ago. Differences between published subspecies were supported genetically. At a local scale, populations were generally considered panmictic with minor genetic structure. Although cheetahs have persisted despite low genetic variability, important questions arise from these findings: Does the cheetah have the ability to adapt to and evolve with future changes in environmental and infectious pressure? How would cheetahs cope with further loss of genetic diversity? Connectivity in the wild should be maintained via prevention of habitat loss, while management of small isolated populations may require reestablishing gene flow. Genetics could assist captive-breeding decisions and provide forensic evidence as to the geographical origin of illegally traded animals.
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Affiliation(s)
| | - Desiré L. Dalton
- National Zoological Gardens of South Africa, Pretoria, South Africa,University of Venda, Thohoyandou, South Africa
| | | | | | | | - Warren E. Johnson
- Smithsonian Conservation Biology Institute, Front Royal, VA, United States
| | | | | | - Antoinette Kotzé
- National Zoological Gardens of South Africa, Pretoria, South Africa,University of Free State South Africa, Bloemfontein, South Africa
| | - Stephen J. O’Brien
- St. Petersburg State University, St. Petersburg, Russia,Nova Southeastern University, Fort Lauderdale, FL, United States
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9
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Janecka JE, Zhang Y, Li D, Munkhtsog B, Bayaraa M, Galsandorj N, Wangchuk TR, Karmacharya D, Li J, Lu Z, Uulu KZ, Gaur A, Kumar S, Kumar K, Hussain S, Muhammad G, Jevit M, Hacker C, Burger P, Wultsch C, Janecka MJ, Helgen K, Murphy WJ, Jackson R. Range-Wide Snow Leopard Phylogeography Supports Three Subspecies. J Hered 2017; 108:597-607. [DOI: 10.1093/jhered/esx044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
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10
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Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (BETHESDA, MD.) 2016; 6:1607-16. [PMID: 27172201 PMCID: PMC4889657 DOI: 10.1534/g3.116.028746] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/23/2016] [Indexed: 01/03/2023]
Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Robert A Grahn
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Aleksey V Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - Victor A David
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702
| | | | | | - Steven Hannah
- Nestlé Purina PetCare Company, St. Louis, Missouri 63134
| | - Sher Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, West Virginia 25443 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Alex Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Stephen J O'Brien
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Pat Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Leslie A Lyons
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
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11
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Mattucci F, Oliveira R, Lyons LA, Alves PC, Randi E. European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation? Ecol Evol 2015; 6:3-22. [PMID: 26811770 PMCID: PMC4716505 DOI: 10.1002/ece3.1815] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 02/03/2023] Open
Abstract
Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over‐hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random‐bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well‐differentiated clusters (average ФST = 0.159, rst = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild‐living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average ФST = 0.103, rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north‐eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene–early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free‐ranging domestic cats along corridor edges should be carefully monitored.
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Affiliation(s)
- Federica Mattucci
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia Bologna Italy
| | - Rita Oliveira
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery College of Veterinary Medicine University of Missouri-Columbia Columbia 65211 Missouri USA
| | - Paulo C Alves
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal; Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana Missoula 59812 Montana USA
| | - Ettore Randi
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia BolognaItaly; Department 18/Section of Environmental Engineering Aalborg University 9000 Aalborg Denmark
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Spencer PBS, Yurchenko AA, David VA, Scott R, Koepfli KP, Driscoll C, O'Brien SJ, Menotti-Raymond M. The Population Origins and Expansion of Feral Cats in Australia. J Hered 2015; 107:104-14. [PMID: 26647063 DOI: 10.1093/jhered/esv095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris).
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Affiliation(s)
- Peter B S Spencer
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond).
| | - Andrey A Yurchenko
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Victor A David
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Rachael Scott
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Klaus-Peter Koepfli
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Carlos Driscoll
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Stephen J O'Brien
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Marilyn Menotti-Raymond
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
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Abstract
Practical relevance: The health of the cat mirrors a complex interaction between its environment (nurture) and its genetics (nature). To date, over 70 genetic mutations (variants) have been defined in the cat; many involve diseases, structural anomalies, coat color and texture, including numerous that are clinically relevant. This trend will continue as more of the feline genome is deciphered. Genetic testing, and eventually whole-genome sequencing, should become routine diagnostic tools in feline healthcare within the foreseeable future. Global importance: Cat breeds have dispersed around the world. Thus, feline medicine clinicians should be aware of breeds common to their region and common mutations found within those regional populations. Random-bred populations of domestic cats can also have defined genetic characteristics and mutations, which are equally worthy of understanding by feline medicine clinicians. Outline: This article reviews the chronology and evolution of genetic and genomic tools pertinent to feline medicine. Possible strategies for mapping genetic traits and defects, and how these impact on feline health, are also discussed. The focus is on three historical periods: (1) research conducted before the availability of the cat genome; (2) research performed immediately after the availability of sequences of the cat genome; and (3) current research that goes beyond one cat genome and utilizes the genome sequences of many cats. Evidence base: The data presented are extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning heritable traits and/or diseases. The authors draw upon their personal experience and expertise in feline genetics.
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Jin W, Wen H, Du X, Zheng J, Gu R. Transcriptome analysis reveals the potential mechanism of the albino skin development in pufferfish Takifugu obscurus. In Vitro Cell Dev Biol Anim 2015; 51:572-7. [DOI: 10.1007/s11626-015-9871-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/14/2015] [Indexed: 01/24/2023]
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Witzenberger KA, Hochkirch A. The genetic integrity of the ex situ population of the European wildcat (Felis silvestris silvestris) is seriously threatened by introgression from domestic cats (Felis silvestris catus). PLoS One 2014; 9:e106083. [PMID: 25162450 PMCID: PMC4146591 DOI: 10.1371/journal.pone.0106083] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022] Open
Abstract
Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.
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Affiliation(s)
- Kathrin A. Witzenberger
- Zoo Hoyerswerda, Hoyerswerda, Germany
- Trier University, Department of Biogeography, Trier, Germany
| | - Axel Hochkirch
- Trier University, Department of Biogeography, Trier, Germany
- * E-mail:
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Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE. Mapping and genotypic analysis of the NK-lysin gene in chicken. Genet Sel Evol 2014; 46:43. [PMID: 25001618 PMCID: PMC4120735 DOI: 10.1186/1297-9686-46-43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/13/2014] [Indexed: 11/10/2022] Open
Abstract
Background Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds. Results A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines. Conclusions The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - James E Womack
- Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA.
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Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Tsuzaki T, Fuji K, Koyama T, Sakamoto T, Araki K. Construction of a radiation hybrid panel and the first yellowtail (Seriola quinqueradiata) radiation hybrid map using a nanofluidic dynamic array. BMC Genomics 2014; 15:165. [PMID: 24571093 PMCID: PMC3943507 DOI: 10.1186/1471-2164-15-165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background Yellowtail (Seriola quinqueradiata) are an economically important species in Japan. However, there are currently no methods for captive breeding and early rearing for yellowtail. Thus, the commercial cultivation of this species is reliant upon the capture of wild immature fish. Given this, there is a need to develop captive breeding techniques to reduce pressure on wild stocks and facilitate the sustainable development of yellowtail aquaculture. We constructed a whole genome radiation hybrid (RH) panel for yellowtail gene mapping and developed a framework physical map using a nanofluidic dynamic array to use SNPs (single nucleotide polymorphisms) in ESTs (expressed sequence tags) for the DNA-assisted breeding of yellowtail. Results Clonal RH cell lines were obtained after ionizing radiation; specifically, 78, 64, 129, 55, 42, and 53 clones were isolated after treatment with 3,000, 4,000, 5,000, 6,000, 8,000, or 10,000 rads, respectively. A total of 421 hybrid cell lines were obtained by fusion with mouse B78 cells. Ninety-four microsatellite markers used in the genetic linkage map were genotyped using the 421 hybrid cell lines. Based upon marker retention and genome coverage, we selected 93 hybrid cell lines to form an RH panel. Importantly, we performed the first genotyping of yellowtail markers in an RH panel using a nanofluidic dynamic array (Fluidigm, CA, USA). Then, 580 markers containing ESTs and SNPs were mapped in the first yellowtail RH map. Conclusions We successfully developed a yellowtail RH panel to facilitate the localization of markers. Using this, a framework RH map was constructed with 580 markers. This high-density physical map will serve as a useful tool for the identification of genes related to important breeding traits using genetic structural information, such as conserved synteny. Moreover, in a comparison of 30 sequences in the RH group 1 (SQ1), yellowtail appeared to be evolutionarily closer to medaka and the green-spotted pufferfish than to zebrafish. We suggest that synteny analysis may be potentially useful as a tool to investigate chromosomal evolution by comparison with model fish.
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Affiliation(s)
- Jun-ya Aoki
- National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie 519-0423, Japan.
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Mattucci F, Oliveira R, Bizzarri L, Vercillo F, Anile S, Ragni B, Lapini L, Sforzi A, Alves PC, Lyons LA, Randi E. Genetic structure of wildcat (Felis silvestris) populations in Italy. Ecol Evol 2013. [DOI: 10.1002/ece3.569] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- F. Mattucci
- Laboratorio di Genetica; ISPRA; Istituto Superiore per la Protezione e la Ricerca Ambientale; Via Cà Fornacetta 9; 40064; Ozzano dell'Emilia; Bologna; Italy
| | - R. Oliveira
- CIBIO/InBIO Laboratório Associado; Centro de Investigação em Biodiversidade e Recursos Genéticos and Dep. de Biologia da Faculdade de Ciências do Porto; Universidade do Porto; Porto; Portugal
| | - L. Bizzarri
- Dipartimento di Biologia Cellulare ed Ambientale; Università degli Studi di Perugia; Via Elce di Sotto; 06123; Perugia; Italy
| | - F. Vercillo
- Dipartimento di Biologia Cellulare ed Ambientale; Università degli Studi di Perugia; Via Elce di Sotto; 06123; Perugia; Italy
| | - S. Anile
- Dipartimento di Biologia Cellulare ed Ambientale; Università degli Studi di Perugia; Via Elce di Sotto; 06123; Perugia; Italy
| | - B. Ragni
- Dipartimento di Biologia Cellulare ed Ambientale; Università degli Studi di Perugia; Via Elce di Sotto; 06123; Perugia; Italy
| | - L. Lapini
- Museo Friulano di Storia Naturale; Via Marangoni 39; 33100; Udine; Italy
| | - A. Sforzi
- Museo di Storia Naturale della Maremma; Strada Corsini 5; 58100; Grosseto; Italy
| | | | - L. A. Lyons
- School of Veterinary Medicine; Population Health and Reproduction; University of California, Davis; One Shields Avenue; 95616; Davis; California
| | - E. Randi
- Laboratorio di Genetica; ISPRA; Istituto Superiore per la Protezione e la Ricerca Ambientale; Via Cà Fornacetta 9; 40064; Ozzano dell'Emilia; Bologna; Italy
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Alhaddad H, Khan R, Grahn RA, Gandolfi B, Mullikin JC, Cole SA, Gruffydd-Jones TJ, Häggström J, Lohi H, Longeri M, Lyons LA. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds. PLoS One 2013; 8:e53537. [PMID: 23308248 PMCID: PMC3538540 DOI: 10.1371/journal.pone.0053537] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/03/2012] [Indexed: 01/21/2023] Open
Abstract
Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.
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Affiliation(s)
- Hasan Alhaddad
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Razib Khan
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Robert A. Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Timothy J. Gruffydd-Jones
- The Feline Centre, School of Veterinary Science, University of Bristol, Langford, Bristol, United Kingdom
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Medicine, University of Helsinki, and The Folkhälsan Research Center, Helsinki, Finland
| | - Maria Longeri
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, Milano, Italy
| | - Leslie A. Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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Applications and techniques for non-invasive faecal genetics research in felid conservation. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0675-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bach LH, Gandolfi B, Grahn JC, Millon LV, Kent MS, Narfstrom K, Cole SA, Mullikin JC, Grahn RA, Lyons LA. A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. Cytogenet Genome Res 2012; 137:7-14. [PMID: 22777158 DOI: 10.1159/000339416] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2012] [Indexed: 11/19/2022] Open
Abstract
The current genetic and recombination maps of the cat have fewer than 3,000 markers and a resolution limit greater than 1 Mb. To complement the first-generation domestic cat maps, support higher resolution mapping studies, and aid genome assembly in specific areas as well as in the whole genome, a 15,000(Rad) radiation hybrid (RH) panel for the domestic cat was generated. Fibroblasts from the female Abyssinian cat that was used to generate the cat genomic sequence were fused to a Chinese hamster cell line (A23), producing 150 hybrid lines. The clones were initially characterized using 39 short tandem repeats (STRs) and 1,536 SNP markers. The utility of whole-genome amplification in preserving and extending RH panel DNA was also tested using 10 STR markers; no significant difference in retention was observed. The resolution of the 15,000(Rad) RH panel was established by constructing framework maps across 10 different 1-Mb regions on different feline chromosomes. In these regions, 2-point analysis was used to estimate RH distances, which compared favorably with the estimation of physical distances. The study demonstrates that the 15,000(Rad) RH panel constitutes a powerful tool for constructing high-resolution maps, having an average resolution of 40.1 kb per marker across the ten 1-Mb regions. In addition, the RH panel will complement existing genomic resources for the domestic cat, aid in the accurate re-assemblies of the forthcoming cat genomic sequence, and support cross-species genomic comparisons.
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Affiliation(s)
- L H Bach
- Population Health and Reproduction,, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
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Two-phase analysis in consensus genetic mapping. G3-GENES GENOMES GENETICS 2012; 2:537-49. [PMID: 22670224 PMCID: PMC3362937 DOI: 10.1534/g3.112.002428] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 03/01/2012] [Indexed: 01/25/2023]
Abstract
Numerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as “synchronized TSP.” The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the entire chromosome or an exact/heuristic algorithm applied subsequently to the revealed small non-overlapping regions with conflicts separated by non-conflicting regions. The proposed approach was tested on a wide range of simulated data and real datasets from maize.
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23
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The Feline Genome and Clinical Implications. THE CAT 2012. [PMCID: PMC7152298 DOI: 10.1016/b978-1-4377-0660-4.00043-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Siberian tiger's recent population bottleneck in the Russian Far East revealed by microsatellite markers. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2011.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Janečka JE, Tewes ME, Laack LL, Caso A, Grassman Jr LI, Haines AM, Shindle DB, Davis BW, Murphy WJ, Honeycutt RL. Reduced genetic diversity and isolation of remnant ocelot populations occupying a severely fragmented landscape in southern Texas. Anim Conserv 2011. [DOI: 10.1111/j.1469-1795.2011.00475.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Eizirik E, David VA, Buckley-Beason V, Roelke ME, Schäffer AA, Hannah SS, Narfström K, O'Brien SJ, Menotti-Raymond M. Defining and mapping mammalian coat pattern genes: multiple genomic regions implicated in domestic cat stripes and spots. Genetics 2010; 184:267-75. [PMID: 19858284 PMCID: PMC2815922 DOI: 10.1534/genetics.109.109629] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/12/2009] [Indexed: 11/18/2022] Open
Abstract
Mammalian coat patterns (e.g., spots, stripes) are hypothesized to play important roles in camouflage and other relevant processes, yet the genetic and developmental bases for these phenotypes are completely unknown. The domestic cat, with its diversity of coat patterns, is an excellent model organism to investigate these phenomena. We have established three independent pedigrees to map the four recognized pattern variants classically considered to be specified by a single locus, Tabby; in order of dominance, these are the unpatterned agouti form called "Abyssinian" or "ticked" (T(a)), followed by Spotted (T(s)), Mackerel (T(M)), and Blotched (t(b)). We demonstrate that at least three different loci control the coat markings of the domestic cat. One locus, responsible for the Abyssinian form (herein termed the Ticked locus), maps to an approximately 3.8-Mb region on cat chromosome B1. A second locus controls the Tabby alleles T(M) and t(b), and maps to an approximately 5-Mb genomic region on cat chromosome A1. One or more additional loci act as modifiers and create a spotted coat by altering mackerel stripes. On the basis of our results and associated observations, we hypothesize that mammalian patterned coats are formed by two distinct processes: a spatially oriented developmental mechanism that lays down a species-specific pattern of skin cell differentiation and a pigmentation-oriented mechanism that uses information from the preestablished pattern to regulate the synthesis of melanin profiles.
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Affiliation(s)
- Eduardo Eizirik
- Department of Ophthalmology, Mason Eye Institute, University of Missouri, Columbia, Missouri 65211, USA.
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Widespread retinal degenerative disease mutation (rdAc) discovered among a large number of popular cat breeds. Vet J 2009; 186:32-8. [PMID: 19747862 DOI: 10.1016/j.tvjl.2009.08.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/15/2009] [Accepted: 08/05/2009] [Indexed: 11/23/2022]
Abstract
The recent discovery of a mutational variant in the CEP290 gene (CEP290: IVS50+9T>G), conferring recessive retinal degeneration in Abyssinian and Somali (long-haired Abyssinian) cats (rdAc) prompted a survey among 41 cat breeds (846 individuals) to assess the incidence, frequency and clinical consequence of rdAc. The rdAc allele displayed widespread distribution, observed in 16/43 (37%) breeds, exhibiting a high allele frequency (∼33%) in North American and European Siamese populations. Clinical evaluations demonstrated high concordance between rdAc pathology and the CEP290 (IVS50+9T>G) homozygous genotype (P=1.1E-6), with clinical disease similar to affected Abyssinians/Somalis. This retinal degeneration has not been reported in breeds other than the Abyssinian/Somali and poses a significant health risk particularly in the Siamese breed group. Alertness of the veterinary community and the present availability of commercial diagnostic testing could synergistically enable breeders to reduce the incidence of rdAc blindness in pure-bred cat populations.
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Hertwig ST, Schweizer M, Stepanow S, Jungnickel A, Böhle UR, Fischer MS. Regionally high rates of hybridization and introgression in German wildcat populations (Felis silvestris, Carnivora, Felidae). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2009.00536.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Menotti-Raymond M, David VA, Eizirik E, Roelke ME, Ghaffari H, O'Brien SJ. Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals. J Hered 2009; 100 Suppl 1:S8-13. [PMID: 19398491 PMCID: PMC3307065 DOI: 10.1093/jhered/esp018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 03/06/2009] [Accepted: 03/16/2009] [Indexed: 11/12/2022] Open
Abstract
The SILVER locus has been mapped in the domestic cat, identifying a unique genomic location distinct from that of any known reported gene associated with silver or hypopigmentation in mammals. A demonstrated lack of linkage to SILV, the strong candidate gene for silver, led to the initiation of a genome scan utilizing 2 pedigrees segregating for silver coat color. Linkage mapping defined a genomic region for SILVER as a 3.3-Mb region, (95.87-99.21 Mb) on chromosome D2, (peak logarithm of the odds = 10.5, = 0), which displays conserved synteny to a genomic interval between 118.58 and 121.85 Mb on chromosome 10 in the human genome. In the domestic cat, mutations at the SILVER locus suppress the development of pigment in the hair, but in contrast to other mammalian silver variants, there is an apparently greater influence on the production of pheomelanin than eumelanin pigment. The mapping of a novel locus for SILVER offers much promise in identifying a gene that may help elucidate aspects of pheomelanogenesis, a pathway that has been very elusive, and illustrates the promise of the cat genome project in increasing our understanding of basic biological processes of general relevance for mammals.
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Affiliation(s)
- Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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Menotti-Raymond M, David VA, Schäffer AA, Tomlin JF, Eizirik E, Phillip C, Wells D, Pontius JU, Hannah SS, O'Brien SJ. An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics 2009; 93:305-13. [PMID: 19059333 PMCID: PMC2656606 DOI: 10.1016/j.ygeno.2008.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 11/03/2008] [Accepted: 11/05/2008] [Indexed: 11/23/2022]
Abstract
We report on the completion of an autosomal genetic linkage (GL) map of the domestic cat (Felis silvestris catus). Unlike two previous linkage maps of the cat constructed with a hybrid pedigree between the domestic cat and the Asian leopard cat, this map was generated entirely with domestic cats, using a large multi-generational pedigree (n=256) maintained by the Nestlé Purina PetCare Company. Four hundred eighty-three simple tandem repeat (STR) loci have been assigned to linkage groups on the cat's 18 autosomes. A single linkage group spans each autosome. The length of the cat map, estimated at 4370 cM, is long relative to most reported mammalian maps. A high degree of concordance in marker order was observed between the third-generation map and the 1.5 Mb-resolution radiation hybrid (RH) map of the cat. Using the cat 1.9x whole-genome sequence, we identified map coordinates for 85% of the loci in the cat assembly, with high concordance observed in marker order between the linkage map and the cat sequence assembly. The present version represents a marked improvement over previous cat linkage maps as it (i) nearly doubles the number of markers that were present in the second-generation linkage map in the cat, (ii) provides a linkage map generated in a domestic cat pedigree which will more accurately reflect recombination distances than previous maps generated in a hybrid pedigree, and (iii) provides single linkage groups spanning each autosome. Marker order was largely consistent between this and the previous maps, though the use of a hybrid pedigree in the earlier versions appears to have contributed to some suppression of recombination. The improved linkage map will provide an added resource for the mapping of phenotypic variation in the domestic cat and the use of this species as a model system for biological research.
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Affiliation(s)
- Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti. Genetics 2009; 181:1415-25. [PMID: 19189955 DOI: 10.1534/genetics.108.095240] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9x whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9x-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.
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32
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Antunes A, Troyer JL, Roelke ME, Pecon-Slattery J, Packer C, Winterbach C, Winterbach H, Hemson G, Frank L, Stander P, Siefert L, Driciru M, Funston PJ, Alexander KA, Prager KC, Mills G, Wildt D, Bush M, O'Brien SJ, Johnson WE. The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics. PLoS Genet 2008; 4:e1000251. [PMID: 18989457 PMCID: PMC2572142 DOI: 10.1371/journal.pgen.1000251] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 10/02/2008] [Indexed: 12/02/2022] Open
Abstract
The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA ΦST = 0.92; nDNA FST = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIVPle subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (∼324,000–169,000 years ago), which expanded during the Late Pleistocene (∼100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (∼14,000–7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIVPle variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently. The lion Panthera leo, a formidable carnivore with a complex cooperative social system, has fascinated humanity since pre-historical times, inspiring hundreds of religious and cultural allusions. Here, we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and Asia. We assayed appropriately informative autosomal, Y-chromosome, and mitochondrial genetic markers, and assessed the prevalence and genetic variation of the lion-specific feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV) that causes AIDS-like immunodeficiency disease in domestic cats. We compare the large multigenic dataset from lions with patterns of genetic variation of the FIVPle to characterize the population-genomic legacy of lions. We refute the hypothesis that African lions consist of a single panmictic population, highlighting the importance of preserving populations in decline rather than prioritizing larger-scale conservation efforts. Interestingly, lion and FIVPle variation revealed evidence of unsuspected genetic diversity even in the well-studied lion population of the Serengeti Ecosystem, which consists of recently admixed animals derived from three distinct genetic groups.
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Affiliation(s)
- Agostinho Antunes
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
- CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
- * E-mail: (AA); (WEJ)
| | - Jennifer L. Troyer
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America
| | - Melody E. Roelke
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - Craig Packer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | | | | | - Graham Hemson
- Wildlife Conservation Research Unit, Tubney, Oxon, United Kingdom
| | - Laurence Frank
- Laikipia Predator Project, Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, United States of America
| | | | - Ludwig Siefert
- Department of Wildlife and Animal Resources Management, Makerere University, Kampala, Uganda
| | | | - Paul J. Funston
- Department of Nature Conservation, Tshwane University of Technology, Pretoria, South Africa
| | - Kathy A. Alexander
- Wildlife Veterinary Unit, Department of Wildlife and National Parks, Kasane, Botswana
| | - Katherine C. Prager
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Gus Mills
- SANParks, Endangered Wildlife Trust and Mammal Research Institute, University of Pretoria, Skukuza, South Africa
| | - David Wildt
- Smithsonian's National Zoological Park, Conservation & Research Center, Front Royal, Virginia, United States of America
| | - Mitch Bush
- Smithsonian's National Zoological Park, Conservation & Research Center, Front Royal, Virginia, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - Warren E. Johnson
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail: (AA); (WEJ)
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A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics 2008; 93:299-304. [PMID: 18951970 DOI: 10.1016/j.ygeno.2008.09.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/21/2008] [Accepted: 09/23/2008] [Indexed: 11/23/2022]
Abstract
We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2662 markers, translating to an estimated average intermarker distance of 939 kilobases (kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence.
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O'Brien SJ, Johnson W, Driscoll C, Pontius J, Pecon-Slattery J, Menotti-Raymond M. State of cat genomics. Trends Genet 2008; 24:268-79. [PMID: 18471926 PMCID: PMC7126825 DOI: 10.1016/j.tig.2008.03.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/26/2008] [Accepted: 03/26/2008] [Indexed: 01/19/2023]
Abstract
Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.
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Ramsdell CM, Lewandowski AA, Glenn JLW, Vrana PB, O'Neill RJ, Dewey MJ. Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus). BMC Evol Biol 2008; 8:65. [PMID: 18302785 PMCID: PMC2266908 DOI: 10.1186/1471-2148-8-65] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 02/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus. RESULTS Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome. CONCLUSION These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).
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Affiliation(s)
- Clifton M Ramsdell
- Department of Genetics and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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Murphy WJ, O'Brien SJ. Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference. Nat Protoc 2008; 2:3022-30. [PMID: 18007639 DOI: 10.1038/nprot.2007.429] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we describe protocols for designing, optimizing and implementing conserved anchor primers for use in genome mapping or phylogenetic applications, with particular emphasis on homologous gene sequences among mammals. The increasing number of whole genome sequences in public databases makes this approach applicable across a wide range of taxa. Genome sequences from representatives of two or more divergent subclades within a taxonomic group of interest are used to identify candidate local alignments (i.e., exons, exons spanning introns or conserved 5'- or 3'-untranslated regions) that contain sequences with appropriate variability for the chosen downstream application. PCR primers are designed to maximize amplification success across a broad range of taxa, and are optimized under a touchdown thermocycling protocol. Based on the initial optimization results, primers are selected for application in a diverse sampling of species, or for mapping the genome of a target species of interest. We discuss factors that have to be considered for experimental design of broad-scope phylogenetic studies. With this protocol, primers can be designed, optimized and implemented within as little as 1-2 weeks.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA.
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Lipinski MJ, Froenicke L, Baysac KC, Billings NC, Leutenegger CM, Levy AM, Longeri M, Niini T, Ozpinar H, Slater MR, Pedersen NC, Lyons LA. The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations. Genomics 2007; 91:12-21. [PMID: 18060738 DOI: 10.1016/j.ygeno.2007.10.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/06/2007] [Accepted: 10/09/2007] [Indexed: 11/17/2022]
Abstract
The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds. The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age.
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Affiliation(s)
- Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California at Davis, Davis, CA 95616, USA
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Borodin PM, Karamysheva TV, Rubtsov NB. Immunofluorescent analysis of meiotic recombination in the domestic cat. ACTA ACUST UNITED AC 2007. [DOI: 10.1134/s1990519x07060065] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Luo SJ, Johnson WE, David VA, Menotti-Raymond M, Stanyon R, Cai QX, Beck T, Yuhki N, Pecon-Slattery J, Smith JLD, O'Brien SJ. Development of Y chromosome intraspecific polymorphic markers in the Felidae. ACTA ACUST UNITED AC 2007; 98:400-13. [PMID: 17646273 DOI: 10.1093/jhered/esm063] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.
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Affiliation(s)
- Shu-Jin Luo
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA.
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Cardone MF, Lomiento M, Teti MG, Misceo D, Roberto R, Capozzi O, D'Addabbo P, Ventura M, Rocchi M, Archidiacono N. Evolutionary history of chromosome 11 featuring four distinct centromere repositioning events in Catarrhini. Genomics 2007; 90:35-43. [PMID: 17490852 DOI: 10.1016/j.ygeno.2007.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 01/14/2007] [Accepted: 01/18/2007] [Indexed: 11/30/2022]
Abstract
Panels of BAC clones used in FISH experiments allow a detailed definition of chromosomal marker arrangement and orientation during evolution. This approach has disclosed the centromere repositioning phenomenon, consisting in the activation of a novel, fully functional centromere in an ectopic location, concomitant with the inactivation of the old centromere. In this study, appropriate panels of BAC clones were used to track the chromosome 11 evolutionary history in primates and nonprimate boreoeutherian mammals. Chromosome 11 synteny was found to be highly conserved in both primate and boreoeutherian mammalian ancestors. Amazingly, we detected four centromere repositioning events in primates (in Old World monkeys, in gibbons, in orangutans, and in the Homo-Pan-Gorilla (H-P-G) clade ancestor), and one in Equidae. Both H-P-G and Lar gibbon novel centromeres were flanked by large duplicons with high sequence similarity. Outgroup species analysis revealed that this duplicon was absent in phylogenetically more distant primates. The chromosome 11 ancestral centromere was probably located near the HSA11q telomere. The domain of this inactivated centromere, in humans, is almost devoid of segmental duplications. An inversion occurred in chromosome 11 in the common ancestor of H-P-G. A large duplicon, again absent in outgroup species, was found located adjacent to the inversion breakpoints. In Hominoidea, almost all the five largest duplicons of this chromosome appeared involved in significant evolutionary architectural changes.
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Murakami T, Maki N, Nishida-Umehara C, Matsuda Y, Agata K. Establishment of high-resolution FISH mapping system and its application for molecular cytogenetic characterization of chromosomes in newt, Cynops pyrrhogaster (Urodela, Amphibia). Chromosome Res 2007; 15:471-84. [PMID: 17525830 DOI: 10.1007/s10577-007-1139-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 04/04/2007] [Accepted: 04/04/2007] [Indexed: 11/29/2022]
Abstract
Urodele amphibians (newts and salamanders) are important animal models for understanding regeneration mechanisms and genome evolution. We constructed ideograms of BrdU/dT- and C-banded karyotypes in the Japanese fire-belly newt, Cynops pyrrhogaster, which is useful as a model animal with extremely high ability of regeneration. We also established a high-resolution FISH mapping system for newts, and localized satellite DNA sequences, 18S rDNAs, telomeric (TTAGGG)n repeats and seven functional genes, including genes associated with lens regeneration, tyrosinase and two types of gamma crystallins, to chromosomes of the newt. The 18S rDNAs were localized to three chromosomal pairs in males, whereas the chromosomal locations were highly variable in females. No hybridization signals were detected for the telomeric (TTAGGG)n sequence. All three lens regeneration-related genes were mapped on the short arm of chromosome 7, suggesting that the location of the genes in the same linkage group may be correlated with the regulation of gene expression associated with chromatin dynamics in interphase nuclei during regeneration. The chromosomal distribution and nucleotide sequences of pericentric satellite DNA sequences were well conserved between C. pyrrhogaster and European newts; in contrast, there was species specificity of nucleotide sequences for centromere-specific satellite DNAs.
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Affiliation(s)
- Takahiro Murakami
- Department of Nutrition and Food Sciences, Ehime Women's College, 421 Ibuki, Uwajima, Ehime, Japan
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43
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Fyfe JC, Kurzhals RL, Hawkins MG, Wang P, Yuhki N, Giger U, Van Winkle TJ, Haskins ME, Patterson DF, Henthorn PS. A complex rearrangement in GBE1 causes both perinatal hypoglycemic collapse and late-juvenile-onset neuromuscular degeneration in glycogen storage disease type IV of Norwegian forest cats. Mol Genet Metab 2007; 90:383-92. [PMID: 17257876 PMCID: PMC2063609 DOI: 10.1016/j.ymgme.2006.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 12/08/2006] [Accepted: 12/08/2006] [Indexed: 01/21/2023]
Abstract
Deficiency of glycogen branching enzyme (GBE) activity causes glycogen storage disease type IV (GSD IV), an autosomal recessive error of metabolism. Abnormal glycogen accumulates in myocytes, hepatocytes, and neurons, causing variably progressive, benign to lethal organ dysfunctions. A naturally occurring orthologue of human GSD IV was described previously in Norwegian forest cats (NFC). Here, we report that while most affected kittens die at or soon after birth, presumably due to hypoglycemia, survivors of the perinatal period appear clinically normal until onset of progressive neuromuscular degeneration at 5 months of age. Molecular investigation of affected cats revealed abnormally spliced GBE1 mRNA products and lack of GBE cross-reactive material in liver and muscle. Affected cats are homozygous for a complex rearrangement of genomic DNA in GBE1, constituted by a 334 bp insertion at the site of a 6.2 kb deletion that extends from intron 11 to intron 12 (g. IVS11+1552_IVS12-1339 del6.2kb ins334 bp), removing exon 12. An allele-specific, PCR-based test demonstrates that the rearrangement segregates with the disease in the GSD IV kindred and is not found in unrelated normal cats. Screening of 402 privately owned NFC revealed 58 carriers and 4 affected cats. The molecular characterization of feline GSD IV will enhance further studies of GSD IV pathophysiology and development of novel therapies in this unique animal model.
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Affiliation(s)
- John C Fyfe
- Laboratory of Comparative Medical Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
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Ishida Y, David VA, Eizirik E, Schäffer AA, Neelam BA, Roelke ME, Hannah SS, O'Brien SJ, Menotti-Raymond M. A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat. Genomics 2006; 88:698-705. [PMID: 16860533 DOI: 10.1016/j.ygeno.2006.06.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/09/2006] [Accepted: 06/12/2006] [Indexed: 11/22/2022]
Abstract
Three proteins have been described in humans and mice as being essential for even distribution, transport, and translocation of pigment granules, with defects in these molecules giving rise to lighter skin/coat color. The dilute phenotype in domestic cats affects both eumelanin and phaeomelanin pigment pathways; for example, black pigmentation combined with dilute appears gray and orange pigments appear cream. The dilute pigmentation segregates as a fully penetrant, autosomal recessive trait. We conducted classical linkage mapping with microsatellites in a large multigeneration pedigree of domestic cats and detected tight linkage for dilute on cat chromosome C1 (theta=0.08, LOD=10.81). Fine-mapping identified a genomic region exhibiting conserved synteny to human chromosome 2, which included one of the three dilute candidate genes, melanophilin (MLPH). Sequence analysis in dilute cats identified a single base pair deletion in exon 2 of MLPH transcripts that introduces a stop codon 11 amino acids downstream, resulting in the truncation of the bulk of the MLPH protein. The occurrence of this homozygous variant in 97 unrelated dilute cats representing 26 cat breeds and random-bred cats, along with 89 unrelated wild-type cats representing 29 breeds and random-bred cats, supports the finding that dilute is caused by this single mutation in MLPH (p<0.00001). Single-nucleotide polymorphism analyses in dilute individuals identified a single haplotype in dilute cats, suggesting that a single mutation event in MLPH gave rise to dilute in domestic cats.
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Affiliation(s)
- Yasuko Ishida
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA.
| | - Victor A David
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA
| | - Eduardo Eizirik
- Centro de Biologia Genômica e Molecular, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Beena A Neelam
- Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702, USA
| | - Melody E Roelke
- Laboratory of Genomic Diversity, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702, USA
| | | | - Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA
| | - Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA.
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WAITS LISETTEP, BUCKLEY-BEASON VALERIEA, JOHNSON WARRENE, ONORATO DAVE, MCCARTHY TOM. A select panel of polymorphic microsatellite loci for individual identification of snow leopards (Panthera uncia). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01591.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, Pearks Wilkerson AJ, Neelam B, O’Brien SJ, Menotti-Raymond M. A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 2006; 89:189-96. [PMID: 16997530 PMCID: PMC3760348 DOI: 10.1016/j.ygeno.2006.08.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/17/2006] [Accepted: 08/17/2006] [Indexed: 11/26/2022]
Abstract
We report the construction of a 1.5-Mb-resolution radiation hybrid map of the domestic cat genome. This new map includes novel microsatellite loci and markers derived from the 2X genome sequence that target previous gaps in the feline-human comparative map. Ninety-six percent of the 1793 cat markers we mapped have identifiable orthologues in the canine and human genome sequences. The updated autosomal and X-chromosome comparative maps identify 152 cat-human and 134 cat-dog homologous synteny blocks. Comparative analysis shows the marked change in chromosomal evolution in the canid lineage relative to the felid lineage since divergence from their carnivoran ancestor. The canid lineage has a 30-fold difference in the number of interchromosomal rearrangements relative to felids, while the felid lineage has primarily undergone intrachromosomal rearrangements. We have also refined the pseudoautosomal region and boundary in the cat and show that it is markedly longer than those of human or mouse. This improved RH comparative map provides a useful tool to facilitate positional cloning studies in the feline model.
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Affiliation(s)
- William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Brian Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Victor A. David
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702
| | - Richa Agarwala
- IEB/NCBI/NLM, National Institutes of Health, Department of Health & Human Services, Bethesda, MD 20894
| | - Alejandro A. Schäffer
- CBB/NCBI/NLM, National Institutes of Health, Department of Health & Human Services, Bethesda, MD 20894
| | - Alison J. Pearks Wilkerson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Beena Neelam
- Advanced Biomedical Computing Center, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Stephen J. O’Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702
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Lyons LA, Bailey SJ, Baysac KC, Byrns G, Erdman CA, Fretwell N, Froenicke L, Gazlay KW, Geary LA, Grahn JC, Grahn RA, Karere GM, Lipinski MJ, Rah H, Ruhe MT, Bach LH. The Tabby cat locus maps to feline chromosome B1. Anim Genet 2006; 37:383-6. [PMID: 16879352 PMCID: PMC1619149 DOI: 10.1111/j.1365-2052.2006.01458.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Tabby markings of the domestic cat are unique coat patterns for which no causative candidate gene has been inferred from other mammals. In this study, a genome scan was performed on a large pedigree of cats that segregated for Tabby coat markings, specifically for the Abyssinian (Ta-) and blotched (tbtb) phenotypes. There was linkage between the Tabby locus and eight markers on cat chromosome B1. The most significant linkage was between marker FCA700 and Tabby (Z = 7.56, θ = 0.03). Two additional markers in the region supported linkage, although not with significant LOD scores. Pairwise analysis of the markers supported the published genetic map of the cat, although additional meioses are required to refine the region. The linked markers cover a 17-cM region and flank an evolutionary breakpoint, suggesting that the Tabby gene has a homologue on either human chromosome 4 or 8. Alternatively, Tabby could be a unique locus in cats.
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Affiliation(s)
- L A Lyons
- Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA.
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48
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Goh G, Raudsepp T, Durkin K, Wagner ML, Schäffer AA, Agarwala R, Tozaki T, Mickelson JR, Chowdhary BP. High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 2006; 89:89-112. [PMID: 16916595 DOI: 10.1016/j.ygeno.2006.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 06/15/2006] [Accepted: 06/19/2006] [Indexed: 12/18/2022]
Abstract
High-resolution physically ordered gene maps for equine homologs of human chromosome 5 (HSA5), viz., horse chromosomes 14 and 21 (ECA14 and ECA21), were generated by adding 179 new loci (131 gene-specific and 48 microsatellites) to the existing maps of the two chromosomes. The loci were mapped primarily by genotyping on a 5000-rad horse x hamster radiation hybrid panel, of which 28 were mapped by fluorescence in situ hybridization. The approximately fivefold increase in the number of mapped markers on the two chromosomes improves the average resolution of the map to 1 marker/0.9 Mb. The improved resolution is vital for rapid chromosomal localization of traits of interest on these chromosomes and for facilitating candidate gene searches. The comparative gene mapping data on ECA14 and ECA21 finely align the chromosomes to sequence/gene maps of a range of evolutionarily distantly related species. It also demonstrates that compared to ECA14, the ECA21 segment corresponding to HSA5 is a more conserved region because of preserved gene order in a larger number of and more diverse species. Further, comparison of ECA14 and the distal three-quarters region of ECA21 with corresponding chromosomal segments in 50 species belonging to 11 mammalian orders provides a broad overview of the evolution of these segments in individual orders from the putative ancestral chromosomal configuration. Of particular interest is the identification and precise demarcation of equid/Perissodactyl-specific features that for the first time clearly distinguish the origins of ECA14 and ECA21 from similar-looking status in the Cetartiodactyls.
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Affiliation(s)
- Glenda Goh
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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49
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Fyfe JC, Menotti-Raymond M, David VA, Brichta L, Schäffer AA, Agarwala R, Murphy WJ, Wedemeyer WJ, Gregory BL, Buzzell BG, Drummond MC, Wirth B, O'Brien SJ. An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res 2006; 16:1084-90. [PMID: 16899656 PMCID: PMC1557767 DOI: 10.1101/gr.5268806] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The leading genetic cause of infant mortality is spinal muscular atrophy (SMA), a clinically and genetically heterogeneous group of disorders. Previously we described a domestic cat model of autosomal recessive, juvenile-onset SMA similar to human SMA type III. Here we report results of a whole-genome scan for linkage in the feline SMA pedigree using recently developed species-specific and comparative mapping resources. We identified a novel SMA gene candidate, LIX1, in an approximately140-kb deletion on feline chromosome A1q in a region of conserved synteny to human chromosome 5q15. Though LIX1 function is unknown, the predicted secondary structure is compatible with a role in RNA metabolism. LIX1 expression is largely restricted to the central nervous system, primarily in spinal motor neurons, thus offering explanation of the tissue restriction of pathology in feline SMA. An exon sequence screen of 25 human SMA cases, not otherwise explicable by mutations at the SMN1 locus, failed to identify comparable LIX1 mutations. Nonetheless, a LIX1-associated etiology in feline SMA implicates a previously undetected mechanism of motor neuron maintenance and mandates consideration of LIX1 as a candidate gene in human SMA when SMN1 mutations are not found.
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Affiliation(s)
- John C Fyfe
- Laboratory of Comparative Medical Genetics, Department of Microbiology & Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA.
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50
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Pukazhenthi BS, Neubauer K, Jewgenow K, Howard J, Wildt DE. The impact and potential etiology of teratospermia in the domestic cat and its wild relatives. Theriogenology 2006; 66:112-21. [PMID: 16644003 DOI: 10.1016/j.theriogenology.2006.03.020] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Teratospermia (production of >60% morphologically abnormal sperm/ejaculate) is relatively common among various species in the family Felidae, which is comprised of 37 species. Over two decades of research in this area have produced a significant understanding of the phenotypic expression, its impacts on sperm function and etiology. There is good evidence suggesting that a reduction in genetic diversity contributes to this phenomenon. Results to date demonstrate that spermatozoa from teratospermic donors are compromised in the ability to undergo capacitation and the acrosome reaction, penetrate the zona-pellucida, fertilize conspecific oocytes and survive cryopreservation. Recent studies also reveal abnormalities in chromatin integrity in sperm from teratospermic donors, which, interestingly, fails to impact fertilization or embryo development after intracytoplasmic sperm injection. Through planned inbreeding studies, we now have established that teratospermic cats also produce more spermatozoa by virtue of more sperm producing tissue, more germ cells per Sertoli cell and reduced germ cell loss during spermatogenesis. Overall, it now is clear that gain in sperm quantity is achieved at the expense of sperm quality, suggesting an extensive disruption of normal testicular function in teratospermic donors. Preliminary studies on testicular gene expression in teratospermic cats have also revealed abnormal expression patterns. These findings have markedly increased our understanding of testis biology in the teratospermic donor and reaffirm the value of cats, including wild species, as models for studying novel regulatory mechanisms controlling spermatogenesis and spermiogenesis.
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Affiliation(s)
- Budhan S Pukazhenthi
- Smithsonian's National Zoological Park, Conservation and Research Center, Front Royal, VA 22630, USA.
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