1
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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2
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Carroll RA, Rice ES, Murphy WJ, Lyons LA, Thibaud-Nissen F, Coghill LM, Swanson WF, Terio KA, Boyd T, Warren WC. A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 2024; 14:8073. [PMID: 38580653 PMCID: PMC10997796 DOI: 10.1038/s41598-024-56003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024] Open
Abstract
The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.
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Affiliation(s)
- Rachel A Carroll
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX, 77843-4458, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon M Coghill
- Bioinformatics and Analytics Core, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William F Swanson
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, 3400 Vine St., Cincinnati, OH, 45220, USA
| | - Karen A Terio
- Zoological Pathology Program, University of Illinois, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Tyler Boyd
- Oklahoma City Zoo and Botanical Garden, 2000 Remington Pl., Oklahoma, OK, 73111, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
- Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
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3
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Qi H, Lim QL, Kinoshita K, Nakajima N, Inoue-Murayama M. A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models. Mol Ecol Resour 2024; 24:e13928. [PMID: 38234258 DOI: 10.1111/1755-0998.13928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.
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Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Qi Luan Lim
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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4
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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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5
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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: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Muscatello LV, Oto ED, Dignazzi M, Murphy WJ, Porcellato I, De Maria R, Raudsepp T, Foschini MP, Sforna M, Benazzi C, Brunetti B. HER2 Overexpression and Amplification in Feline Pulmonary Carcinoma. Vet Pathol 2021; 58:527-530. [PMID: 33461438 DOI: 10.1177/0300985820988147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
HER2 is overexpressed, amplified, and mutated in a subset of human lung cancer. The aim of this study was to investigate HER2 protein overexpression and gene amplification in feline pulmonary carcinomas. Thirteen pulmonary carcinomas were selected and TTF-1 and HER2 expression was evaluated by immunohistochemistry. Fluorescence in situ hybridization (FISH) was performed with a HER2 probe and a BAC probe for the feline chromosome E1p1.12-p1.11 region. Twelve adenocarcinomas and 1 squamous cell carcinoma were diagnosed. TTF-1 was positive in 7 carcinomas (58%). HER2 was overexpressed in 2 (15%), equivocal in 5 (38%), and negative in 6 cases (46%). FISH analysis of HER2 was indeterminate in 2 cases. Three pulmonary carcinomas (27%) had HER2 amplification and 8 cases were not amplified (73%). The significant correlation between HER2 protein overexpression and gene amplification are promising preliminary data, but study of additional cases is needed to confirm HER2 as a target for possible innovative treatments.
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7
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Affiliation(s)
- Wengang Zhang
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Jeffrey J. Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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8
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Armstrong EE, Taylor RW, Miller DE, Kaelin CB, Barsh GS, Hadly EA, Petrov D. Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biol 2020; 18:3. [PMID: 31915011 PMCID: PMC6950864 DOI: 10.1186/s12915-019-0734-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.
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Affiliation(s)
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA
- End2EndGenomics, LLC, Davis, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Seattle Children's Hospital and The University of Washington, Seattle, WA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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Samaha G, Beatty J, Wade CM, Haase B. The Burmese cat as a genetic model of type 2 diabetes in humans. Anim Genet 2019; 50:319-325. [PMID: 31179570 DOI: 10.1111/age.12799] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
The recent extension of genetic tools to the domestic cat, together with the serendipitous consequences of selective breeding, have been essential to the study of the genetic diseases that affect them. Cats are increasingly presented for veterinary surveillance and share many of human's heritable diseases, allowing them to serve as natural models of these conditions. Feline diabetes mellitus is a common condition in domestic cats that bears close pathological and clinical resemblance to type 2 diabetes in humans, including pancreatic β-cell dysfunction and peripheral insulin resistance. In Australia, New Zealand and Europe, diabetes mellitus is almost four times more common in cats of the Burmese breed than in other breeds. This geographically based breed predisposition parallels familial and population clustering of type 2 diabetes in humans. As a genetically isolated population, the Australian Burmese breed provides a spontaneous, naturally occurring genetic model of type 2 diabetes. Genetically isolated populations typically exhibit extended linkage disequilibrium and increased opportunity for deleterious variants to reach high frequencies over many generations due to genetic drift. Studying complex diseases in such populations allows for tighter control of confounding factors including environmental heterogeneity, allelic frequencies and population stratification. The homogeneous genetic background of Australian Burmese cats may provide a unique opportunity to either refine genetic signals previously associated with type 2 diabetes or identify new risk factors for this disease.
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Affiliation(s)
- G Samaha
- Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - J Beatty
- Sydney School of Veterinary Science, Valentine Charlton Cat Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - C M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - B Haase
- Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
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10
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Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 2019; 10:E409. [PMID: 31142040 PMCID: PMC6627929 DOI: 10.3390/genes10060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William H Wadlington
- Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA.
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jeremy T Stutchman
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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11
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Muscatello LV, Di Oto E, Sarli G, Monti V, Foschini MP, Benazzi C, Brunetti B. HER2 Amplification Status in Feline Mammary Carcinoma: A Tissue Microarray-Fluorescence In Situ Hydridization-Based Study. Vet Pathol 2018; 56:230-238. [PMID: 30384816 DOI: 10.1177/0300985818808531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) is a tyrosine kinase receptor overexpressed in a subset of breast cancer due to HER2 gene amplification. HER2 protein is expressed in feline mammary carcinomas, but little is known about its cytogenetic alterations. The aim of this study was to evaluate HER2 gene amplification status and its correlation with HER2 protein expression in feline mammary carcinomas. Feline mammary carcinomas were retrospectively selected and immunohistochemically (IHC) evaluated for HER2 protein expression. All the HER2 IHC-positive (3+) and equivocal (2+) cases and a subset of negative cases (0/1+) were selected for fluorescence in situ hybridization (FISH). Dual-core tissue microarrays were prepared for FISH. IHC and FISH were evaluated according to the 2013 American Society of Clinical Oncology/College of American Pathologists guidelines. The study included 107 feline mammary carcinomas from 88 queens. HER2 protein expression was positive (3+) in 7 cases (6.5%), equivocal (2+) in 48 cases (45%), and negative (0/1+) in 52 cases (48.5%). HER2 status was indeterminate in 8 feline mammary carcinomas (12%), amplified in 3 (4%), equivocal in 4 (6%), and nonamplified in 53 (78%). HER2 gene amplification and protein expression were significantly positively correlated ( R = 0.283; P < .0001). HER2 gene is amplified in a subset of feline mammary carcinomas despite the HER2 positive or equivocal protein expression, but it remains to be determined if the HER2 amplification is a gene alteration that drives mammary tumor carcinogenesis or only a bystander passenger mutation.
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Affiliation(s)
- Luisa Vera Muscatello
- 1 Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy.,These authors contributed equally to this work
| | - Enrico Di Oto
- 2 Molecular Pathology-Anatomic Pathology Laboratory, Oncological Institute "F.Addarii"-S. Orsola Hospital, Bologna, Italy.,These authors contributed equally to this work
| | - Giuseppe Sarli
- 1 Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | | | - Maria Pia Foschini
- 4 Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Cinzia Benazzi
- 1 Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Barbara Brunetti
- 1 Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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12
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Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, Xiong Z, Kim J, Zhang G, Trut LN, Larkin DM, Kukekova AV. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes (Basel) 2018; 9:E308. [PMID: 29925783 PMCID: PMC6027122 DOI: 10.3390/genes9060308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/19/2018] [Accepted: 06/04/2018] [Indexed: 01/08/2023] Open
Abstract
The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Marta Farré
- Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK.
| | - Michael P Robson
- Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Naomi B Won
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jennifer L Johnson
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ronak Buch
- Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Estelle R Bastounes
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Xueyan Xiang
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Shaohong Feng
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Shiping Liu
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Zijun Xiong
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Jaebum Kim
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
| | - Guojie Zhang
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Denis M Larkin
- Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK.
| | - Anna V Kukekova
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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13
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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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14
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Perelman PL, Pichler R, Gaggl A, Larkin DM, Raudsepp T, Alshanbari F, Holl HM, Brooks SA, Burger PA, Periasamy K. Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000 RAD and 15000 RAD. Sci Rep 2018; 8:1982. [PMID: 29386528 PMCID: PMC5792482 DOI: 10.1038/s41598-018-20223-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
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Affiliation(s)
- Polina L Perelman
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
- Institute of Molecular and Cellular Biology and Novosibirsk State University, Novosibirsk, Russia
| | - Rudolf Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Anna Gaggl
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | | | | | | | | | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni, Vienna, Austria
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria.
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15
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Marques C, Correia J, Ferreira F. HER2-positive feline mammary carcinoma. Aging (Albany NY) 2018; 8:1574-5. [PMID: 27518031 PMCID: PMC5032681 DOI: 10.18632/aging.101015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Cláudia Marques
- Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Jorge Correia
- Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Fernando Ferreira
- Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
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16
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:993-1014. [PMID: 29157065 DOI: 10.1080/24701394.2017.1404041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.
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Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Myreya Pinedo-Castro
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Joseph Mark Shostell
- b Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
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17
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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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18
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Murata C, Sawaya H, Nakata K, Yamada F, Imoto I, Kuroiwa A. The cryptic Y-autosome translocation in the small Indian mongoose, Herpestes auropunctatus, revealed by molecular cytogenetic approaches. Chromosoma 2016; 125:807-15. [PMID: 26743516 DOI: 10.1007/s00412-015-0572-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 12/16/2015] [Accepted: 12/28/2015] [Indexed: 11/27/2022]
Abstract
In initial studies of the eutherian small Indian mongoose (Herpestes auropunctatus), the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Previous reports indicated that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome. However, it has been difficult to identify the chromosomes that harbor the translocated Y chromosomal segment because it is an extremely small euchromatic region. Using a Southern blot analysis, we detected four conserved Y-linked genes, SRY, EIF2S3Y, KDM5D, and ZFY, in the male genome. We cloned homologues of these genes and determined their sequences, which showed high homology to genes in two carnivore species, cat and dog. To unambiguously identify the Y-bearing autosome, we performed immunostaining of pachytene spermatocytes using antibodies against SYCP3, γH2AX, and the centromere. We observed trivalent chromosomes, and the associations between the distal ends of the chromosomes were consistent with those of Y and X1 chromosomes. The centromere of the Y chromosome was located on the ancestral Y chromosomal segment. We mapped the complementary DNA (cDNA) clones of these genes to the male chromosomes using fluorescence in situ hybridization (FISH), and the linear localization of all genes was confirmed by two-colored FISH. These Y-linked genes were localized to the proximal region of the long arm of a single telomeric chromosome, and we successfully identified the chromosome harboring the ancestral Y chromosomal segment.
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Affiliation(s)
- Chie Murata
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hirohito Sawaya
- Graduate School of Life Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Katsushi Nakata
- Yambaru Wildlife Conservation Center, Ministry of the Environment, 263-1 Hiji, Kunigami-son, Kunigami-gun, Okinawa, 905-1413, Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Asato Kuroiwa
- Laboratory of Animal Cytogenetics, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.
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19
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Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res 2016; 26:1-11. [PMID: 26518481 PMCID: PMC4691742 DOI: 10.1101/gr.186668.114] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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20
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The 14/15 association as a paradigmatic example of tracing karyotype evolution in New World monkeys. Chromosoma 2015; 125:747-56. [DOI: 10.1007/s00412-015-0565-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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21
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Rodgers TW, Giacalone J, Heske EJ, Janečka JE, Jansen PA, Phillips CA, Schooley RL. Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics. J Mammal 2015. [DOI: 10.1093/jmammal/gyu012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, O’Brien SJ. Annotated features of domestic cat - Felis catus genome. Gigascience 2014; 3:13. [PMID: 25143822 PMCID: PMC4138527 DOI: 10.1186/2047-217x-3-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 07/23/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors. FINDINGS Here we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus. CONCLUSIONS The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.
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Affiliation(s)
- Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Serguei Simonov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Alexey Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Anton Logachev
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Andrey Shevchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Nikolay Cherkasov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Anton Svitin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Joan Pontius
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
| | - Carlos A Driscoll
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA
| | - Kevin Blackistone
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA
| | - Cristina Barr
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA
| | - David Goldman
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA
| | - Agostinho Antunes
- CIIMAR — Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, n. 289, 4050–123 Porto, Portugal
| | - Javier Quilez
- Department of Animal and Food Science, Veterinary Molecular Genetics Service, Universitat Autónoma de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Belen Lorente-Galdos
- IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, PRBB (The Barcelona Biomedical Research Park), 08003 Barcelona, Catalonia, Spain
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey
| | - Tomas Marques-Bonet
- IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, PRBB (The Barcelona Biomedical Research Park), 08003 Barcelona, Catalonia, Spain
| | - Marylin Menotti-Raymond
- Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, 21702 Frederick, MD, USA
| | - Victor A David
- Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, 21702 Frederick, MD, USA
| | - Kristina Narfström
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, 08028 Columbia, MO, USA
| | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, 33004 Ft Lauderdale, FL, USA
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Abstract
Over 200 hereditary diseases have been identified and reported in the cat, several of which affect the eye, with homology to human hereditary disease. Compared with traditional murine models, the cat demonstrates more features in common with humans, including many anatomic and physiologic similarities, longer life span, increased size, and a genetically more heterogeneous background. The development of genomic resources in the cat has facilitated mapping and further characterization of feline models. During recent years, the wealth of knowledge in feline ophthalmology and neurophysiology has been extended to include new diseases of significant interest for comparative ophthalmology. This makes the cat an extremely valuable animal species to utilize for further research into disease processes affecting both cats and humans. This is especially true in the advancement and study of new treatment regimens and for extended therapeutic trials. Groups of feline eye diseases reviewed in the following are lysosomal storage disorders, congenital glaucoma, and neuroretinal degenerations. Each has important implications for human ophthalmic research.
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Affiliation(s)
- Kristina Narfström
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri 65201;
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The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family. ANNALS OF ANIMAL SCIENCE 2012. [DOI: 10.2478/v10220-012-0001-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae FamilyGenome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.
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25
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Avila F, Das PJ, Kutzler M, Owens E, Perelman P, Rubes J, Hornak M, Johnson WE, Raudsepp T. Development and application of camelid molecular cytogenetic tools. J Hered 2012; 105:858-69. [PMID: 23109720 DOI: 10.1093/jhered/ess067] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human-camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly.
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Affiliation(s)
- Felipe Avila
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Pranab J Das
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Michelle Kutzler
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Elaine Owens
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Polina Perelman
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Jiri Rubes
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Miroslav Hornak
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Warren E Johnson
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Terje Raudsepp
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak).
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26
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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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27
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Kaelin CB, Xu X, Hong LZ, David VA, McGowan KA, Schmidt-Küntzel A, Roelke ME, Pino J, Pontius J, Cooper GM, Manuel H, Swanson WF, Marker L, Harper CK, van Dyk A, Yue B, Mullikin JC, Warren WC, Eizirik E, Kos L, O'Brien SJ, Barsh GS, Menotti-Raymond M. Specifying and sustaining pigmentation patterns in domestic and wild cats. Science 2012; 337:1536-41. [PMID: 22997338 DOI: 10.1126/science.1220893] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.
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28
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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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29
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Raudsepp T, Das PJ, Avila F, Chowdhary BP. The pseudoautosomal region and sex chromosome aneuploidies in domestic species. Sex Dev 2011; 6:72-83. [PMID: 21876343 DOI: 10.1159/000330627] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The pseudoautosomal region (PAR) is a unique and specialized segment on the mammalian sex chromosomes with known functions in male meiosis and fertility. Detailed molecular studies of the region in human and mouse show dramatic differences between the 2 PARs. Recent mapping efforts in horse, dog/cat, cattle/ruminants, pig and alpaca indicate that the PAR also varies in size and gene content between other species. Given that PAR genes escape X inactivation, these differences might critically affect the genetic consequences, such as embryonic survival and postnatal phenotypes of sex chromosome aneuploidies. The aim of this review is to combine the available information about the organization of the PAR in domestic species with the cytogenetic data on sex chromosome aneuploidies. We show that viable XO individuals are relatively frequently found in species with small PARs, such as horses, humans and mice but are rare or absent in species in which the PAR is substantially larger, like in cattle/ruminants, dogs, pigs, and alpacas. No similar correlation can be detected between the PAR size and the X chromosome trisomy in different species. Recent evidence about the likely involvement of PAR genes in placenta formation, early embryonic development and genomic imprinting are presented.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA.
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30
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Baptista CS, Bastos E, Santos S, Gut IG, Guedes-Pinto H, Gärtner F, Chaves R. TWIST1 Gene: First Insights in Felis catus. Curr Genomics 2011; 11:212-20. [PMID: 21037858 PMCID: PMC2878985 DOI: 10.2174/138920210791110933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 11/22/2022] Open
Abstract
TWIST1 is thought to be a novel oncogene. Understanding the molecular mechanisms regulating the TWIST1 gene expression profiles in tumor cells may give new insights regarding prognostic factors and novel therapeutic targets in veterinary oncology. In the present study we partially isolated the TWIST1 gene in Felis catus and performed comparative studies. Several primer combinations were used based on the alignments of homologous DNA sequences. After PCR amplification, three bands were obtained, purified and sequenced. Several bioinformatic tools were utilized to carry out the comparative studies. Higher similarity was found between the isolated TWIST1 gene in Felis catus and Homo sapiens (86%) than between Homo sapiens and Rattus norvegicus or Mus musculus (75%). Partial amino acid sequence showed no change in the four species analyzed. This confirmed that coding sequences presented high similarity (~96%) between man and cat. These results give the first insights regarding the TWIST1 gene in cat but further studies are required in order to establish, or not, its role in tumor formation and progression in veterinary oncology.
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Affiliation(s)
- Cláudia S Baptista
- Department of Veterinary Clinics, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Largo Prof. Abel Salazar, 2, 4099-003 Porto, Portugal
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31
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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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32
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Volleth M, Yang F, Müller S. High-resolution chromosome painting reveals the first genetic signature for the chiropteran suborder Pteropodiformes (Mammalia: Chiroptera). Chromosome Res 2011; 19:507-19. [DOI: 10.1007/s10577-011-9196-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/18/2011] [Accepted: 02/18/2011] [Indexed: 01/18/2023]
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33
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Sathyamurthy G, Swamy NR. Computational Identification of Putative miRNAs from Felis Catus. Biomed Eng Comput Biol 2010. [DOI: 10.4137/becb.s5233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
microRNAs represent a class of noncoding small RNAs of approximately 20–23 nt length, which are evolutionarily conserved and play a vital role in various biological processes by either degrading or repressing mRNA translation. The Felis catus (cat) genome sequence has been published, and just revealed the number of miRNAs in the genome–-without mention of any further details on these miRNAs. This paper discusses an in silico comparative approach using all known sequences of vertebrate pre-miRNA as query sequence, and report 405 putative miRNAs from cat genome. We determine the identity values of pre-miRNAs and mature miRNAs besides statistical sequence characteristics. Interestingly, among 405 miRNAs–-90, 53 and 50 showed 100% identity to cattle, human and dog, respectively. Further, we have validated 6 miRNAs, whose identity are <85% with the query sequence and validated them using MiPred algorithm. We also identify 25 miRNA clusters in cat based on their homologs in other vertebrates. Most importantly, based on identities among pre-miRNA, mature miRNA, miRNA families and clusters, we observe that miRNAs from cat are more identical to cattle, than humans. Our results, therefore may add a new dimension to the studies related to the evolution of cat.
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34
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Menotti-Raymond M, Deckman KH, David V, Myrkalo J, O'Brien SJ, Narfström K. Mutation discovered in a feline model of human congenital retinal blinding disease. Invest Ophthalmol Vis Sci 2010; 51:2852-9. [PMID: 20053974 PMCID: PMC2891453 DOI: 10.1167/iovs.09-4261] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/29/2009] [Accepted: 12/24/2009] [Indexed: 01/12/2023] Open
Abstract
PURPOSE To elucidate the gene defect in a pedigree of cats segregating for autosomal dominant rod-cone dysplasia (Rdy), a retinopathy characterized extensively from a clinical perspective. Disease expression in Rdy cats is comparable to that in young patients with congenital blindness (Leber congenital amaurosis [LCA] or retinitis pigmentosa [RP]). METHODS A pedigree segregating for Rdy was generated and phenotyped by clinical ophthalmic examination methods including ophthalmoscopy and full-field flash electroretinography. Short tandem repeat loci tightly linked to candidate genes for autosomal dominant retinitis pigmentosa in humans were genotyped in the pedigree. RESULTS Significant linkage was established to the candidate gene CRX (LOD = 5.56, = 0) on cat chromosome E2. A single base pair deletion was identified in exon 4 (n.546delC) in affected individuals but not in unaffected littermates. This mutation generates a frame shift in the transcript, introducing a premature stop codon truncating the putative CRX peptide, which would eliminate the critical transcriptional activation region. Clinical observations corroborate previously reported clinical reports about Rdy. Results show that the cone photoreceptor system was more severely affected than the rods in the early disease process. CONCLUSIONS A putative mutation causative of the Rdy phenotype has been described as a single base pair deletion in exon 4 of the CRX gene, thus identifying the first animal model for CRX-linked disease that closely resembles the human disease. As such, it will provide valuable insights into the mechanisms underlying these diseases and their variable presentation, as well as providing a suitable model for testing therapies for these diseases.
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Affiliation(s)
- Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA.
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35
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Philipp U, Steinmetz A, Distl O. Development of Feline Microsatellites and SNPs for Evaluating Primary Cataract Candidate Genes as Cause for Cataract in Angolan Lions (Panthera leo bleyenberghi). J Hered 2010; 101:633-8. [DOI: 10.1093/jhered/esq040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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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: 36] [Impact Index Per Article: 2.6] [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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Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. Chromosome Res 2009; 17:987-1000. [PMID: 19941159 DOI: 10.1007/s10577-009-9096-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/24/2009] [Accepted: 10/26/2009] [Indexed: 01/13/2023]
Abstract
Injection-site-associated sarcomas (ISAS), commonly arising at the site of routine vaccine administration, afflict as many as 22,000 domestic cats annually in the USA. These tumors are typically more aggressive and prone to recurrence than spontaneous sarcomas (non-ISAS), generally receiving a poorer long-term prognosis and warranting a more aggressive therapeutic approach. Although certain clinical and histological factors are highly suggestive of ISAS, timely diagnosis and optimal clinical management may be hindered by the absence of definitive markers that can distinguish between tumors with underlying injection-related etiology and their spontaneous counterpart. Specific nonrandom chromosome copy number aberrations (CNAs) have been associated with the clinical behavior of a vast spectrum of human tumors, providing an extensive resource of potential diagnostic and prognostic biomarkers. Although similar principles are now being applied with great success in other species, their relevance to feline molecular oncology has not yet been investigated in any detail. We report the construction of a genomic microarray platform for detection of recurrent CNAs in feline tumors through cytogenetic assignment of 210 large-insert DNA clones selected at intervals of approximately 15 Mb from the feline genome sequence assembly. Microarray-based profiling of 19 ISAS and 27 non-ISAS cases identified an extensive range of genomic imbalances that were highly recurrent throughout the combined panel of 46 sarcomas. Deletions of two specific regions were significantly associated with the non-ISAS phenotype. Further characterization of these regions may ultimately permit molecular distinction between ISAS and non-ISAS, as a tool for predicting tumor behavior and prognosis, as well as refining means for therapeutic intervention.
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Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping. PLoS One 2009; 4:e7465. [PMID: 19829706 PMCID: PMC2759293 DOI: 10.1371/journal.pone.0007465] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/23/2009] [Indexed: 12/02/2022] Open
Abstract
Background Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes. Methodology/Principal Findings We isolated 214 clones containing 159 orthologs of well conserved single-copy genes of a sequenced lepidopteran model, the silkworm, Bombyx mori, from a BAC library of a sphingid with an unexplored genome, the tobacco hornworm, Manduca sexta. We then constructed a BAC-FISH karyotype identifying all 28 chromosomes of M. sexta by mapping 124 loci using the corresponding BAC clones. BAC probes from three M. sexta chromosomes also generated clear signals on the corresponding chromosomes of the convolvulus hawk moth, Agrius convolvuli, which belongs to the same subfamily, Sphinginae, as M. sexta. Conclusions/Significance Comparison of the M. sexta BAC physical map with the linkage map and genome sequence of B. mori pointed to extensive conserved synteny including conserved gene order in most chromosomes. Only a few rearrangements, including three inversions, three translocations, and two fission/fusion events were estimated to have occurred after the divergence of Bombycidae and Sphingidae. These results add to accumulating evidence for the stability of lepidopteran genomes. Generating signals on A. convolvuli chromosomes using heterologous M. sexta probes demonstrated that BAC-FISH with orthologous sequences can be used for karyotyping a wide range of related and genetically uncharacterized species, significantly extending the ability to develop synteny maps for comparative and functional genomics.
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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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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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Kukekova AV, Vorobieva NV, Beklemisheva VR, Johnson JL, Temnykh SV, Yudkin DV, Trut LN, Andre C, Galibert F, Aguirre GD, Acland GM, Graphodatsky AS. Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes. ACTA ACUST UNITED AC 2009; 100 Suppl 1:S42-53. [PMID: 19546120 DOI: 10.1093/jhered/esp037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.
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Affiliation(s)
- Anna V Kukekova
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, 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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