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Szynwelski BE, Kretschmer R, Matzenbacher CA, Ferrari F, Alievi MM, de Freitas TRO. Hybridization in Canids-A Case Study of Pampas Fox ( Lycalopex gymnocercus) and Domestic Dog ( Canis lupus familiaris) Hybrid. Animals (Basel) 2023; 13:2505. [PMID: 37570312 PMCID: PMC10417603 DOI: 10.3390/ani13152505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Hybridization between species with different evolutionary trajectories can be a powerful threat to wildlife conservation. Anthropogenic activities, such as agriculture and livestock, have led to the degradation and loss of natural habitats for wildlife. Consequently, the incidence of interspecific hybridization between wild and domestic species has increased, although cases involving species of different genera are rare. In Vacaria, a Southern city in Brazil, a female canid with a strange phenotype, which had characteristics between the phenotype of the domestic dog (Canis familiaris) and that of the pampas fox (Lycalopex gymnocercus), was found. Our analysis suggests that the animal is a hybrid between a domestic dog and a pampas fox, but future studies are necessary to investigate additional cases of this hybridization in nature. This finding worries for the conservation of wild canids in South America, especially concerning Lycalopex species. Hybridization with the domestic dog may have harmful effects on pampas fox populations due to the potential for introgression and disease transmission by the domestic dog. Therefore, future studies to explore the consequences of hybridization on genetics, ecology, and behavior of wild populations will be essential to improve the conservation of this species.
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Affiliation(s)
- Bruna Elenara Szynwelski
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Pelotas 96010-900, Rio Grande do Sul, Brazil
| | - Cristina Araujo Matzenbacher
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
| | - Flávia Ferrari
- Núcleo de Conservação e Reabilitação de Animais Silvestres, Universidade Federal do Rio Grande do Sul, Porto Alegre 90540-000, Rio Grande do Sul, Brazil; (F.F.); (M.M.A.)
| | - Marcelo Meller Alievi
- Núcleo de Conservação e Reabilitação de Animais Silvestres, Universidade Federal do Rio Grande do Sul, Porto Alegre 90540-000, Rio Grande do Sul, Brazil; (F.F.); (M.M.A.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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Fan H, Wu Q, Wei F, Yang F, Ng BL, Hu Y. Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution. Genome Biol 2019; 20:267. [PMID: 31810476 PMCID: PMC6898958 DOI: 10.1186/s13059-019-1889-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. RESULTS Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. CONCLUSIONS We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.
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Affiliation(s)
- Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bee Ling Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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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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Mazzatenta A, Carluccio A, Robbe D, Giulio CD, Cellerino A. The companion dog as a unique translational model for aging. Semin Cell Dev Biol 2017; 70:141-153. [DOI: 10.1016/j.semcdb.2017.08.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
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6
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Beklemisheva VR, Perelman PL, Lemskaya NA, Kulemzina AI, Proskuryakova AA, Burkanov VN, Graphodatsky AS. The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora). PLoS One 2016; 11:e0147647. [PMID: 26821159 PMCID: PMC4731086 DOI: 10.1371/journal.pone.0147647] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/06/2016] [Indexed: 11/18/2022] Open
Abstract
Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.
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Affiliation(s)
- Violetta R. Beklemisheva
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Polina L. Perelman
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Natalya A. Lemskaya
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia I. Kulemzina
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia A. Proskuryakova
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir N. Burkanov
- Department of Higher Vertebrates Ecology, Kamchatka Branch of Pacific Geographical Institute of Far East Branch of Russian Academy of Sciences, Petropavlovsk-Kamchatski, Russia
- National Marine Mammal Laboratory, Alaska Fisheries Science Centre, National Marine Fisheries Service, Seattle, Washington, United States of America
| | - Alexander S. Graphodatsky
- Department of Comparative Genomics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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7
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Tanomtong A, Chaiyaphan P, Supanuam P, Puramongkol T, Maneechot N, Jangsuwan N. The Standard Karyotype of the Asiatic Jackal, Canis aureus (Carnivora, Canidae) from Thailand. CYTOLOGIA 2015. [DOI: 10.1508/cytologia.80.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Alongklod Tanomtong
- Applied Taxonomic Research Center (ATRC), Department of Biology, Faculty of Science, Khon Kaen University
| | - Prapakorn Chaiyaphan
- Applied Taxonomic Research Center (ATRC), Department of Biology, Faculty of Science, Khon Kaen University
| | - Praween Supanuam
- Biology Program, Faculty of Science, Ubonratchatani Rajabhat University
| | - Therdsak Puramongkol
- Faculty of Agro-Industrial Technology, Rajamangala University of Technology Tawan-ok
| | - Nuntiya Maneechot
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University
| | - Nantana Jangsuwan
- Applied Biology Program, Faculty of Science and Technology, Thepsatri Rajabhat University
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8
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Zurano JP, Ojeda DS, Bidau CJ, Molina WF, Ledesma MA, Martinez PA. A comparison of heterochromatic regions in three species of neotropical canids. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2014.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kociucka B, Sosnowski J, Kubiak A, Nowak A, Pawlak P, Szczerbal I. Three-dimensional positioning of B chromosomes in fibroblast nuclei of the red fox and the chinese raccoon dog. Cytogenet Genome Res 2013; 139:243-9. [PMID: 23485799 DOI: 10.1159/000348434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 11/19/2022] Open
Abstract
Great progress has been achieved over the last years in studies on chromosome arrangement in mammalian cell nuclei. Growing evidence indicates that the genome's spatial organization is of functional relevance. So far, no attention has been paid to the nuclear organization of B chromosomes (Bs). In this study we have examined nuclear positioning of Bs in 2 species from the Canidae family--the red fox and the Chinese raccoon dog. Using 2D and 3D fluorescence in situ hybridization and 2 gene-specific probes (C-KIT and PDGFRA), we analyzed the location of Bs in fibroblast nuclei. We found that small Bs of the red fox occupied mostly the interior of the nucleus, while medium-sized Bs of the Chinese raccoon dog were observed in the peripheral area of the nucleus as well as in intermediate and interior locations. The more uniform distribution of B chromosomes in the Chinese raccoon dog may be the result of differences in their size, since 3 morphological types of Bs are distinguished in this species. Our results indicate that 3D positioning of B chromosomes in fibroblast nuclei of the 2 canid species is in agreement with the chromosome size-dependent theory.
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Affiliation(s)
- B Kociucka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
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10
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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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Perelman P, Beklemisheva V, Yudkin D, Petrina T, Rozhnov V, Nie W, Graphodatsky A. Comparative Chromosome Painting in Carnivora and Pholidota. Cytogenet Genome Res 2012; 137:174-93. [DOI: 10.1159/000341389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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12
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Chaves R, Louzada S, Meles S, Wienberg J, Adega F. Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus. Chromosome Res 2012; 20:673-83. [PMID: 22847644 DOI: 10.1007/s10577-012-9304-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022]
Abstract
The order Rodentia and in particular the Muridae are characterised by extremely high rates of chromosome evolution and remarkable chromosome diversity. The Praomys group (Murinae, Muridae and Rodentia) constitutes a diverse and abundant group divided into two complexes, the jacksoni complex and the tullbergi complex which includes the species Praomys tullbergi. Comparative chromosome painting using the two index genomes, Mus musculus and Rattus norvegicus, was performed resulting in a high resolution chromosome map for P. tullbergi. The combined use of rat and mouse probes and the assistance of the assembly of all the available sequencing data from Ensembl genome browser allowed a great dissection of P. tullbergi genome, the detection of inversion events and ultimately the refinement of P. tullbergi comparative map. A key achievement was the reconstruction of a high precision Muroidea ancestral karyotype (Muridae/Cricetidae and Murine) based in a broad species analysis combining previous reported comparative maps together with the presented data. This permitted the reconstruction of the evolutionary history of chromosome changes since the ancestral Muroidea genome and enlightened the phylogenetic relationships with the related species mouse and rat. The analysis of constitutive heterochromatin and its co-localisation with the identified evolutionary breakpoints regions was performed suggesting the involvement of repetitive sequences in the chromosome rearrangements that originated the present P. tullbergi genome architecture.
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Affiliation(s)
- Raquel Chaves
- Centre of Genomics and Biotechnology, Institute for Biotechnology and Bioengineering, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), Vila Real, Portugal.
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Popa A, Samollow P, Gautier C, Mouchiroud D. The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol 2012; 4:412-22. [PMID: 22417915 PMCID: PMC3318449 DOI: 10.1093/gbe/evs023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Meiotic recombination is an important evolutionary force shaping the nucleotide landscape of genomes. For most vertebrates, the frequency of recombination varies slightly or considerably between the sexes (heterochiasmy). In humans, male, rather than female, recombination rate has been found to be more highly correlated with the guanine and cytosine (GC) content across the genome. In the present study, we review the results in human and extend the examination of the evolutionary impact of heterochiasmy beyond primates to include four additional eutherian mammals (mouse, dog, pig, and sheep), a metatherian mammal (opossum), and a bird (chicken). Specifically, we compared sex-specific recombination rates (RRs) with nucleotide substitution patterns evaluated in transposable elements. Our results, based on a comparative approach, reveal a great diversity in the relationship between heterochiasmy and nucleotide composition. We find that the stronger male impact on this relationship is a conserved feature of human, mouse, dog, and sheep. In contrast, variation in genomic GC content in pig and opossum is more strongly correlated with female, rather than male, RR. Moreover, we show that the sex-differential impact of recombination is mainly driven by the chromosomal localization of recombination events. Independent of sex, the higher the RR in a genomic region and the longer this recombination activity is conserved in time, the stronger the bias in nucleotide substitution pattern, through such mechanisms as biased gene conversion. Over time, this bias will increase the local GC content of the region.
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Nie W, Wang J, Su W, Wang D, Tanomtong A, Perelman PL, Graphodatsky AS, Yang F. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting. Heredity (Edinb) 2011; 108:17-27. [PMID: 22086079 PMCID: PMC3238119 DOI: 10.1038/hdy.2011.107] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species.
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Affiliation(s)
- W Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan, PR
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15
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Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. Chromosome Res 2011; 19:685-708. [DOI: 10.1007/s10577-011-9233-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 12/27/2022]
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Kovalskaya Y, Aniskin V, Bogomolov P, Surov A, Tikhonov I, Tikhonova G, Robinson T, Volobouev V. Karyotype Reorganisation in the subtilis Group of Birch Mice (Rodentia, Dipodidae, Sicista): Unexpected Taxonomic Diversity within a Limited Distribution. Cytogenet Genome Res 2011; 132:271-88. [DOI: 10.1159/000322823] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2010] [Indexed: 11/19/2022] Open
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17
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Osborne AJ, Brauning R, Schultz JK, Kennedy MA, Slate J, Gemmell NJ. Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora. Mol Ecol Resour 2010; 11:503-13. [PMID: 21481208 DOI: 10.1111/j.1755-0998.2010.02962.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species. These correlations are sometimes driven by a subset of markers, and it is unclear whether this is because those markers best reflect genome-wide heterozygosity, or whether they are linked to fitness-related genes. Differentiating between these scenarios is hindered when the genomic location of markers is unknown. Here, we develop a predicted genomic map of pinniped microsatellite loci based on conservation of primary sequence and genomic location between dog, cat and giant panda. We mapped 210 of 260 (81%) microsatellites from pinnipeds to locations in dog, cat and giant panda genomes. Based on the demonstrable synteny between the genomes of closely related taxa within the Carnivora, we use these data to identify those microsatellites with the greatest chance of cross-species amplification success and demonstrate successful amplification of 21 of 26 loci for cat, dog and two seal species. We also demonstrate the potential to identify candidate genes that may underpin the functional relationship with individual fitness. Overall, we show that this approach provides a rapid and robust method to elucidate genome organisation for nonmodel organisms and have established a resource that facilitates further genetic research on pinnipeds that also has wider applicability to other carnivores.
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Affiliation(s)
- Amy J Osborne
- Department of Anatomy and Structural Biology, Centre for Reproduction and Genomics, University of Otago, Dunedin, New Zealand.
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18
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Kulemzina I, Biltueva LS, Trifonov VA, Perelman PL, Staroselec YY, Beklemisheva VR, Vorobieva NV, Serdukova NA, Graphodatsky AS. Comparative cytogenetics of main Laurasiatheria taxa. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410090322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Swier VJ, Bradley RD, Rens W, Elder FFB, Baker RJ. Patterns of chromosomal evolution in Sigmodon, evidence from whole chromosome paints. Cytogenet Genome Res 2009; 125:54-66. [PMID: 19617697 DOI: 10.1159/000218747] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2009] [Indexed: 11/19/2022] Open
Abstract
Of the superfamily Muroidea (31 genera, 1578 species), the Sigmodontinae (74 genera, 377 species) is the second largest subfamily in number of species and represents a significant radiation of rodent biodiversity. Only 2 of the 74 genera are found in both North and South America (Sigmodon and Oryzomys) and the remainder are exclusively from South America. In recent molecular studies, the genus Sigmodon (Cricetidae, Sigmodontinae) has been considered sister to many other South American Sigmodontines [Steppan et al., 2004]. We examine the chromosomal evolution of 9 species of Sigmodon utilizing chromosomal paints isolated from S. hispidus, proposed to be similar to the ancestral karyotype [Elder, 1980]. Utilizing a phylogenetic hypothesis of a molecular phylogeny of Sigmodon [Henson and Bradley, 2009], we mapped shared chromosomal rearrangements of taxa on a molecular tree to estimate the evolutionary position of each rearrangement. For several species (S. hirsutus, S. leucotis, S. ochrognathus, S. peruanus, and S. toltecus), the karyotype accumulated few or no changes, but in three species (S. arizonae, S. fulviventer, and S. mascotensis) numerous karyotype rearrangements were observed. These rearrangements involved heterochromatic additions, centric fusions, tandem fusions, pericentric inversions, as well as the addition of interstitial DNA not identified by chromosome paints or C-banding. The hypothesis that the ancestral karyotype for this complex had a diploid number of 52, a fundamental number of 52, and a G-band pattern of which most, if not all are similar to that present in modern day S. hispidus fails to be rejected. This hypothesis remains viable as an explanation of chromosomal evolution in Sigmodontine rodents.
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Affiliation(s)
- V J Swier
- Department of Biological Sciences and Museum, Texas Tech University, Lubbock, Tex., USA.
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20
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Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes. Chromosome Res 2008; 16:1215-31. [DOI: 10.1007/s10577-008-1270-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/25/2008] [Accepted: 09/25/2008] [Indexed: 01/10/2023]
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21
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A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics 2008; 93:299-304. [PMID: 18951970 DOI: 10.1016/j.ygeno.2008.09.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/21/2008] [Accepted: 09/23/2008] [Indexed: 11/23/2022]
Abstract
We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2662 markers, translating to an estimated average intermarker distance of 939 kilobases (kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence.
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22
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O'Brien SJ, Johnson W, Driscoll C, Pontius J, Pecon-Slattery J, Menotti-Raymond M. State of cat genomics. Trends Genet 2008; 24:268-79. [PMID: 18471926 PMCID: PMC7126825 DOI: 10.1016/j.tig.2008.03.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/26/2008] [Accepted: 03/26/2008] [Indexed: 01/19/2023]
Abstract
Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.
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23
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Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting. Chromosome Res 2008; 16:129-43. [DOI: 10.1007/s10577-007-1203-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Yuhki N, Beck T, Stephens R, Neelam B, O'Brien SJ. Comparative genomic structure of human, dog, and cat MHC: HLA, DLA, and FLA. ACTA ACUST UNITED AC 2007; 98:390-9. [PMID: 17675392 DOI: 10.1093/jhered/esm056] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Comparisons of the genomic structure of 3 mammalian major histocompatibility complexes (MHCs), human HLA, canine DLA, and feline FLA revealed remarkable structural differences between HLA and the other 2 MHCs. The 4.6-Mb HLA sequence was compared with the 3.9-Mb DLA sequence from 2 supercontigs generated by 7x whole-genome shotgun assembly and 3.3-Mb FLA draft sequence. For FLA, we confirm that 1) feline FLA was split into 2 pieces within the TRIM (member of the tripartite motif) gene family found in human HLA, 2) class II, III, and I regions were placed in the pericentromeric region of the long arm of chromosome B2, and 3) the remaining FLA was located in subtelomeric region of the short arm of chromosome B2. The exact same chromosome break was found in canine DLA structure, where class II, III, and I regions were placed in a pericentromeric region of chromosome 12 whereas the remaining region was located in a subtelomeric region of chromosome 35, suggesting that this chromosome break occurred once before the split of felid and canid more than 55 million years ago. However, significant differences were found in the content of genes in both pericentromeric and subtelomeric regions in DLA and FLA, the gene number, and amplicon structure of class I genes plus 2 other class I genes found on 2 additional chromosomes; canine chromosomes 7 and 18 suggest the dynamic nature in the evolution of MHC class I genes.
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Affiliation(s)
- Naoya Yuhki
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.
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25
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Pardini A, O'Brien P, Fu B, Bonde R, Elder F, Ferguson-Smith M, Yang F, Robinson T. Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria. Proc Biol Sci 2007; 274:1333-40. [PMID: 17374594 PMCID: PMC1914331 DOI: 10.1098/rspb.2007.0088] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.
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Affiliation(s)
- A.T Pardini
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - P.C.M O'Brien
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - B Fu
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - R.K Bonde
- U.S. Geological Survey, Florida Integrated Science CentreGainesville, FL 32605-3574, USA
| | - F.F.B Elder
- Department of Pathology, Cytogenetics LaboratoryUT Southwestern Medical Centre, Dallas, TX 75235, USA
| | - M.A Ferguson-Smith
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - F Yang
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - T.J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
- Author for correspondence ()
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26
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Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, Pearks Wilkerson AJ, Neelam B, O’Brien SJ, Menotti-Raymond M. A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 2007; 89:189-96. [PMID: 16997530 PMCID: PMC3760348 DOI: 10.1016/j.ygeno.2006.08.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/17/2006] [Accepted: 08/17/2006] [Indexed: 11/26/2022]
Abstract
We report the construction of a 1.5-Mb-resolution radiation hybrid map of the domestic cat genome. This new map includes novel microsatellite loci and markers derived from the 2X genome sequence that target previous gaps in the feline-human comparative map. Ninety-six percent of the 1793 cat markers we mapped have identifiable orthologues in the canine and human genome sequences. The updated autosomal and X-chromosome comparative maps identify 152 cat-human and 134 cat-dog homologous synteny blocks. Comparative analysis shows the marked change in chromosomal evolution in the canid lineage relative to the felid lineage since divergence from their carnivoran ancestor. The canid lineage has a 30-fold difference in the number of interchromosomal rearrangements relative to felids, while the felid lineage has primarily undergone intrachromosomal rearrangements. We have also refined the pseudoautosomal region and boundary in the cat and show that it is markedly longer than those of human or mouse. This improved RH comparative map provides a useful tool to facilitate positional cloning studies in the feline model.
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Affiliation(s)
- William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Brian Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Victor A. David
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702
| | - Richa Agarwala
- IEB/NCBI/NLM, National Institutes of Health, Department of Health & Human Services, Bethesda, MD 20894
| | - Alejandro A. Schäffer
- CBB/NCBI/NLM, National Institutes of Health, Department of Health & Human Services, Bethesda, MD 20894
| | - Alison J. Pearks Wilkerson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Beena Neelam
- Advanced Biomedical Computing Center, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Stephen J. O’Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702
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27
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Buckley-Beason VA, Johnson WE, Nash WG, Stanyon R, Menninger JC, Driscoll CA, Howard J, Bush M, Page JE, Roelke ME, Stone G, Martelli PP, Wen C, Ling L, Duraisingam RK, Lam PV, O'Brien SJ. Molecular evidence for species-level distinctions in clouded leopards. Curr Biol 2007; 16:2371-6. [PMID: 17141620 PMCID: PMC5618441 DOI: 10.1016/j.cub.2006.08.066] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 08/18/2006] [Accepted: 08/21/2006] [Indexed: 11/17/2022]
Abstract
Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).
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28
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Szczerbal I, Klukowska-Roetzler J, Dolf G, Schelling C, Switonski M. FISH mapping of 10 canine BAC clones harbouring genes and microsatellites in the arctic fox and the Chinese raccoon dog genomes. J Anim Breed Genet 2006; 123:337-42. [PMID: 16965407 DOI: 10.1111/j.1439-0388.2006.00608.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cytogenetic mapping of the arctic fox and the Chinese raccoon dog were performed using a set of canine probes derived from the Bacterial Artificial Chromosome (BAC) library. Altogether, 10 BAC clones containing sequences of selected genes (PAX3, HBB, ATP2A2, TECTA, PIT1, ABCA4, ESR2, TPH1, HTR2A, MAOA) and microsatellites were mapped by fluorescence in situ hybridization (FISH) experiments to chromosomes of the canids studied. At present, the cytogenetic map on the arctic fox and Chinese raccoon dog consists of 45 loci each. Chromosomal localization of the BAC clones was in agreement with data obtained by earlier independent comparative chromosome painting. However, two events of telomere-to-centromere inversions were tentatively identified while compared with assignments in the dog karyotype.
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Affiliation(s)
- I Szczerbal
- Department of Animal Genetics and Breeding, August Cieszkowski Agricultural University of Poznan, Poznan, Poland
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29
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Goh G, Raudsepp T, Durkin K, Wagner ML, Schäffer AA, Agarwala R, Tozaki T, Mickelson JR, Chowdhary BP. High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 2006; 89:89-112. [PMID: 16916595 DOI: 10.1016/j.ygeno.2006.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 06/15/2006] [Accepted: 06/19/2006] [Indexed: 12/18/2022]
Abstract
High-resolution physically ordered gene maps for equine homologs of human chromosome 5 (HSA5), viz., horse chromosomes 14 and 21 (ECA14 and ECA21), were generated by adding 179 new loci (131 gene-specific and 48 microsatellites) to the existing maps of the two chromosomes. The loci were mapped primarily by genotyping on a 5000-rad horse x hamster radiation hybrid panel, of which 28 were mapped by fluorescence in situ hybridization. The approximately fivefold increase in the number of mapped markers on the two chromosomes improves the average resolution of the map to 1 marker/0.9 Mb. The improved resolution is vital for rapid chromosomal localization of traits of interest on these chromosomes and for facilitating candidate gene searches. The comparative gene mapping data on ECA14 and ECA21 finely align the chromosomes to sequence/gene maps of a range of evolutionarily distantly related species. It also demonstrates that compared to ECA14, the ECA21 segment corresponding to HSA5 is a more conserved region because of preserved gene order in a larger number of and more diverse species. Further, comparison of ECA14 and the distal three-quarters region of ECA21 with corresponding chromosomal segments in 50 species belonging to 11 mammalian orders provides a broad overview of the evolution of these segments in individual orders from the putative ancestral chromosomal configuration. Of particular interest is the identification and precise demarcation of equid/Perissodactyl-specific features that for the first time clearly distinguish the origins of ECA14 and ECA21 from similar-looking status in the Cetartiodactyls.
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Affiliation(s)
- Glenda Goh
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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30
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Abstract
Sequencing of the dog genome allows an investigation of the location-dependent evolutionary processes that occurred since the common ancestor of primates and carnivores, approximately 95 million years ago. We investigated variations in G+C nucleotide fraction and synonymous nucleotide substitution rates (Ks) across dog and human genomes. Our results show that dog genes located either in subtelomeric and pericentromeric regions, or in short synteny blocks, possess significantly elevated G+C fraction and Ks values. Human subtelomeric, but not pericentromeric, genes also exhibit these elevations. We then examined 1.048 Gb of human sequence that is likely not to have been located near a primate telomere at any time since the common ancestor of dog and human. We observed that regions of highest G+C or Ks ("hotspots"; median sizes of 0.5 or 1.3 Mb, respectively) within this sequence were preferentially segregated to dog subtelomeres and pericentromeres during the rearrangements that eventually gave rise to the extant canine karyotype. Our data cannot be accounted for solely on the basis of gradually elevating G+C fractions in subtelomeric regions as a consequence of biased gene conversion. Rather, we propose that high G+C sequences are found preferentially within dog subtelomeres as a direct consequence of chromosomal fission occurring more frequently within regions elevated in G+C.
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Affiliation(s)
- Caleb Webber
- MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.
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31
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Dobigny G, Aniskin V, Granjon L, Cornette R, Volobouev V. Recent radiation in West African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes. Heredity (Edinb) 2006; 95:358-68. [PMID: 16106262 DOI: 10.1038/sj.hdy.6800730] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
West African gerbils of the genus Taterillus constitute a complex of seven sibling species distributed from sudano-guinean to saharo-sahelian regions. They display radically rearranged karyotypes despite low genic divergence and a very recent differentiation, that is, within the last 0.4 Myr for the six most derived species. We here provide a comparison of the seven specific karyotypes and perform a cladistic analysis using chromosomal rearrangements character states. When a posteriori polarized mutations were mapped onto the phylogenetic tree, 38 rearrangements were identified as fixed during the evolution of these rodents. This makes Taterillus one of the most striking examples of accelerated chromosomal evolution within placental mammals. Taking into account the types of chromosomal changes involved, divergence times between lineages, genetic distances, as well as reassessed geographic distributions, we suggest that (1) speciation in West African Taterillus was driven by chromosomal changes, and (2) the paleoclimatic oscillations of the Sahara desert have played a major role in their evolution. In particular, elevated plasticity of the Taterillus genome, as suggested by the patterns observed for some repetitive elements, would have led to a higher probability of mutation. We hypothesize that the process underpinning cladogenesis most probably involved highly underdominant genomic rearrangements that were fixed following pronounced populational bottlenecks resulting from drastic climatic and subsequent environmental changes. Major African rivers formed significant barriers to dispersal, limiting expansion during the more moist and so favorable periods. This scenario would explain the current parapatric species distributions and their relationship to the West African hydrographic features.
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Affiliation(s)
- G Dobigny
- Muséum National d'Histoire Naturelle, Laboratoire Origine, Structure et Evolution de la Biodiversité, FRE CNRS 2695, 55, rue Buffon, Paris F75005, France.
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32
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Abstract
The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.
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Affiliation(s)
- Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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33
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Dobigny G, Yang F, O'Brien PCM, Volobouev V, Kovács A, Pieczarka JC, Ferguson-Smith MA, Robinson TJ. Low rate of genomic repatterning in Xenarthra inferred from chromosome painting data. Chromosome Res 2005; 13:651-63. [PMID: 16235115 DOI: 10.1007/s10577-005-1002-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/18/2005] [Indexed: 10/25/2022]
Abstract
Comparative cytogenetic studies on Xenarthra, one of the most basal mammalian clades in the Placentalia, are virtually absent, being restricted largely to descriptions of conventional karyotypes and diploid numbers. We present a molecular cytogenetic comparison of chromosomes from the two-toed (Choloepus didactylus, 2n = 65) and three-toed sloth species (Bradypus tridactylus, 2n = 52), an anteater (Tamandua tetradactyla, 2n = 54) which, together with some data on the six-banded armadillo (Euphractus sexcinctus, 2n = 58), collectively represent all the major xenarthran lineages. Our results, based on interspecific chromosome painting using flow-sorted two-toed sloth chromosomes as painting probes, show the sloth species to be karyotypically closely related but markedly different from the anteater. We also test the synteny disruptions and segmental associations identified within Pilosa (anteaters and sloths) against the chromosomes of the six-banded armadillo as outgroup taxon. We could thus polarize the 35 non-ambiguously identified chromosomal changes characterizing the evolution of the anteater and sloth genomes and map these to a published sequence-based phylogeny for the group. These data suggest a low rate of genomic repatterning when placed in the context of divergence estimates based on molecular and fossil data. Finally, our results provide a glimpse of a likely ancestral karyotype for the extant Xenarthra, a pivotal group for understanding eutherian genome evolution.
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Affiliation(s)
- G Dobigny
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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34
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Biltueva LS, Yang F, Vorobieva NV, Graphodatsky AS. Comparative map between the domestic pig and dog. Mamm Genome 2005; 15:809-18. [PMID: 15520883 DOI: 10.1007/s00335-004-2391-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Accepted: 06/10/2004] [Indexed: 10/26/2022]
Abstract
Cross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig. In total 98 conserved autosomal segments between pig and dog were detected by probes specific for the 38 autosomes and X Chromosome of the dog. Further integration of our results with the published human--dog and cat--dog comparative maps, and with data from comparative gene mapping, increases the resolution of the current pig--human comparative map. It allows for the conserved syntenies detected in the pig, human, and cat to be aligned against the putative ancestral karyotype of eutherian mammals and for the history of karyotype evolution of the pig lineage to be reconstructed. Fifteen fusions, 17 fissions, and 23 inversions are required to convert the ancestral mammalian karyotype into the extant karyotype of the pig.
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Affiliation(s)
- L S Biltueva
- Institute of Cytology and Genetics, Novosibirsk, Russia
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35
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Brinkmeyer-Langford C, Raudsepp T, Lee EJ, Goh G, Schäffer AA, Agarwala R, Wagner ML, Tozaki T, Skow LC, Womack JE, Mickelson JR, Chowdhary BP. A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 2005; 16:631-49. [PMID: 16180145 DOI: 10.1007/s00335-005-0023-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 04/28/2005] [Indexed: 11/25/2022]
Abstract
A high-resolution (1 marker/700 kb) physically ordered radiation hybrid (RH) and comparative map of 122 loci on equine homologs of human Chromosome 19 (HSA19) shows a variant evolution of these segments in equids/Perissodactyls compared with other mammals. The segments include parts of both the long and the short arm of horse Chromosome 7 (ECA7), the proximal part of ECA21, and the entire short arm of ECA10. The map includes 93 new markers, of which 89 (64 gene-specific and 25 microsatellite) were genotyped on a 5000-rad horse x hamster RH panel, and 4 were mapped exclusively by FISH. The orientation and alignment of the map was strengthened by 21 new FISH localizations, of which 15 represent genes. The approximately sevenfold-improved map resolution attained in this study will prove extremely useful for candidate gene discovery in the targeted equine chromosomal regions. The highlight of the comparative map is the fine definition of homology between the four equine chromosomal segments and corresponding HSA19 regions specified by physical coordinates (bp) in the human genome sequence. Of particular interest are the regions on ECA7 and ECA21 that correspond to the short arm of HSA19-a genomic rearrangement discovered to date only in equids/Perissodactyls as evidenced through comparative Zoo-FISH analysis of the evolution of ancestral HSA19 segments in eight mammalian orders involving about 50 species.
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Affiliation(s)
- Candice Brinkmeyer-Langford
- 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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36
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Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 2005; 309:613-7. [PMID: 16040707 DOI: 10.1126/science.1111387] [Citation(s) in RCA: 392] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.
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37
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Perelman PL, Graphodatsky AS, Serdukova NA, Nie W, Alkalaeva EZ, Fu B, Robinson TJ, Yang F. Karyotypic conservatism in the suborder Feliformia (Order Carnivora). Cytogenet Genome Res 2005; 108:348-54. [PMID: 15627756 DOI: 10.1159/000081530] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Accepted: 07/28/2004] [Indexed: 11/19/2022] Open
Abstract
Multidirectional comparative chromosome painting was used to investigate the karyotypic relationships among representative species from three Feliformia families of the order Carnivora (Viverridae, Hyaenidae and Felidae). Complete sets of painting probes derived from flow-sorted chromosomes of the domestic dog, American mink, and human were hybridized onto metaphases of the spotted hyena (Crocuta crocuta, 2n = 40) and masked palm civet (Paguma larvata, 2n = 44). Extensive chromosomal conservation is evident in these two species when compared with the cat karyotype, and only a few events of chromosome fusion, fission and inversion differentiate the karyotypes of these Feliformia species. The comparative chromosome painting data have enabled the integration of the hyena and palm civet chromosomes into the previously established comparative map among the domestic cat, domestic dog, American mink and human and improved our understanding on the karyotype phylogeny of Feliformia species.
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Affiliation(s)
- P L Perelman
- Institute of Cytology and Genetics, Novosibirsk, Russia
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38
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Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ. Insertional polymorphisms of endogenous feline leukemia viruses. J Virol 2005; 79:3979-86. [PMID: 15767400 PMCID: PMC1061563 DOI: 10.1128/jvi.79.7.3979-3986.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one autosomal locus, B4q15, was enFeLV present in both homologues of all four cats. A single enFeLV occurred in the X chromosome of the Burmese cat, while three to five enFeLV proviruses occurred in each Y chromosome. The X chromosome and nine autosomal enFeLV loci were telomeric, suggesting that ectopic recombination between nonhomologous subtelomeres may contribute to enFeLV distribution. Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats.
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Affiliation(s)
- Alfred L Roca
- Laboratory of Genomic Diversity, Basic Research Program, SAIC-Frederick, Maryland, USA.
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39
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Pienkowska-Schelling A, Zawada M, Schelling C. A canine X chromosome painting probe applied to four canid species: close relationship of a heterochromatic-like sequence between the dog and the blue fox. J Anim Breed Genet 2005; 122 Suppl 1:54-9. [PMID: 16130457 DOI: 10.1111/j.1439-0388.2005.00509.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microdissection of chromosomes is an invaluable tool to physically isolate single chromosomes, chromosome-arms or chromosome-bands and, subsequently generate painting probes with which numerical or structural aberrations of chromosomes can be studied. In addition, such painting probes can be used to compare karyotypic relationships among mammalian species. For the present study a canine whole X chromosome painting probe was prepared by means of conventional microdissection and degenerate-oligonucleotide-primed PCR. The application of this paint to the chromosomes of the domestic dog, red fox, blue fox and Chinese raccoon dog revealed hybridization to the entire X chromosome and the pseudo-autosomal region of the Y chromosome in all four species analysed. In the blue fox the same paint revealed additional strong hybridization signals on the heterochromatic arms after low-stringent posthybridization washes. The present study indicates the existence of an ancient canid heterochromatic-like DNA sequence, which survived in the proximal part of the X chromosome of all species studied and, in addition, was involved in the formation of heterochromatic arms in the blue fox.
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Affiliation(s)
- A Pienkowska-Schelling
- Department of Animal Genetics and Breeding, Agricultural University of Poznan, Poznan, Poland
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40
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Abstract
The gross organization of the genome of Eutheria (placental mammals) into chromosomes follows a simple architecture that, with some minor changes, is almost completely conserved for more than 100 million years in various species of almost all extant mammalian orders. Recent molecular cytogenetic results--especially those from the assumed oldest clade, the Afrotheria--suggest an ancestral karyotype that would calculate the "default" frequency of gross rearrangements to less than two changes within 10 million years of mammalian evolution. The main changes are the fission, movement and subsequent fusion of large chromosome segments or of chromosome arms. Reciprocal translocations are the exception. Chromosome numbers may have increased or decreased significantly in this fusion/fission process but, in most instances, the main architecture still remains evident. There are, however, some exceptions in mammals with extremely derived karyotypes.
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Affiliation(s)
- Johannes Wienberg
- Institute of Human Genetics, GSF-National Research Center for Environment and Health, and Institute for Anthropology and Human Genetics, Department Biology II, Ludwig-Maximilians University, Munich, Germany.
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41
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Abstract
The relatively new field of phylogenomics is beginning to reveal the potential of genomic data for evolutionary studies. As the cost of whole genome sequencing falls, anticipation of complete genome sequences from divergent species, reflecting the major lineages of modern mammals, is no longer a distant dream. In this article, we describe how comparative genomic data from mammals is progressing to resolve long-standing phylogenetic controversies, to refine dogma on how chromosomes evolve and to guide annotation of human and other vertebrate genomes.
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Affiliation(s)
- William J Murphy
- Basic Research Laboratory, SAIC-Frederick, Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.
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Beck TW, Menninger J, Murphy WJ, Nash WG, O'brien SJ, Yuhki N. The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 2004; 56:702-9. [PMID: 15592824 DOI: 10.1007/s00251-004-0742-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 10/19/2004] [Indexed: 10/26/2022]
Abstract
In order to determine the genomic organization of the major histocompatibility complex (MHC) of the domestic cat (Felis catus), DNA probes for 61 markers were designed from human MHC reference sequences and used to construct feline MHC BAC contig map spanning ARE1 in the class II region to the olfactory receptor complex in the extended class I region. Selected BAC clones were then used to identify feline-specific probes for the three regions of the mammalian MHC (class II-class III-class I) for radiation hybrid mapping and fluorescent in situ hybridization to refine the organization of the domestic cat MHC. The results not only confirmed that the p-arm of domestic cat B2 is inverted relative to human Chromosome 6, but also demonstrated that one inversion breakpoint localized to the distal segment of the MHC class I between TRIM39 and TRIM26. The inversion thus disjoined the approximately 2.85 Mb of MHC containing class II-class III-class I (proximal region) from the approximately 0.50 Mb of MHC class I/extended class I region, such that TRIM39 is adjacent to the Chromosome B2 centromere and TRIM26 is adjacent to the B2 telomere in the domestic cat.
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Affiliation(s)
- Thomas W Beck
- Basic Research Program, SAIC-Frederick, National Cancer Institute-Frederick, Frederick, MD, 21702-1201, USA.
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43
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Froenicke L. Origins of primate chromosomes – as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences. Cytogenet Genome Res 2004; 108:122-38. [PMID: 15545724 DOI: 10.1159/000080810] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Accepted: 02/06/2004] [Indexed: 11/19/2022] Open
Abstract
This review examines recent advances in comparative eutherian cytogenetics, including Zoo-FISH data from 30 non-primate species. These data provide insights into the nature of karyotype evolution and enable the confident reconstruction of ancestral primate and boreo-eutherian karyotypes with diploid chromosome numbers of 48 and 46 chromosomes, respectively. Nine human autosomes (1, 5, 6, 9, 11, 13, 17, 18, and 20) represent the syntenies of ancestral boreo-eutherian chromosomes and have been conserved for about 95 million years. The average rate of chromosomal exchanges in eutherian evolution is estimated to about 1.9 rearrangements per 10 million years (involving 3.4 chromosome breaks). The integrated analysis of Zoo-FISH data and alignments of human and mouse draft genome sequences allow the identification of breakpoints involved in primate evolution. Thus, the boundaries of ancestral eutherian conserved segments can be delineated precisely. The mapping of rearrangements onto the phylogenetic tree visualizes landmark chromosome rearrangements, which might have been involved in cladogenesis in eutherian evolution.
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Affiliation(s)
- L Froenicke
- California National Primate Research Center & School of Veterinary Medicine, University of California Davis, 95616, USA.
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Nie W, Wang J, Perelman P, Graphodatsky AS, Yang F. Comparative chromosome painting defines the karyotypic relationships among the domestic dog, Chinese raccoon dog and Japanese raccoon dog. Chromosome Res 2004; 11:735-40. [PMID: 14712859 DOI: 10.1023/b:chro.0000005760.03266.29] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54 + 2-3 B) and Japanese raccoon dog (Nyctereutes p. viverrinus, 2n = 38 + 3-4 B) are two subspecies of the same species. The genome-wide comparative chromosome map between the Japanese raccoon dog and domestic dog (Canis familiaris) has been established by fluorescence in-situ hybridization with a set of domestic dog painting probes. In this study, we established the comparative chromosome map for the Chinese raccoon dog and domestic dog. In total, dog probes specific for the 38 autosomes delineated 41 conserved chromosomal segments in the Chinese raccoon dog. Probes from dog chromosomes 1, 13 and 19 each painted two Chinese raccoon dog chromosome segments. Fifteen dog autosomal probes each hybridized to one Chinese raccoon dog chromosome, while each of the other dog autosomal probes painted to a single Chinese raccoon dog chromosomal arm. Dog X chromosome probe delineated the entire X chromosome of the Chinese raccoon dog; the dog Y chromosome probe hybridized to the pseudoautosomal region at the Xpter as well as the entire Y chromosome of the Chinese raccoon dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in the genomes of the Chinese and Japanese raccoon dogs demonstrates that their differences in the karyotypes of these two subspecies could have resulted from eight Robertsonian translocations. The large difference in chromosome number between the Chinese and Japanese raccoon dogs suggests that they should be considered as two distinct species.
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Affiliation(s)
- Wenhui Nie
- Key Laboratory of Cellular & Molecular Evolution, The Chinese Academy of Sciences, Kunming, Yunnan, Peoples Republic of China
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45
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Zrzavý J, Řičánková V. Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets. ZOOL SCR 2004. [DOI: 10.1111/j.0300-3256.2004.00152.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Dobigny G, Ozouf-Costaz C, Bonillo C, Volobouev V. Evolution of rRNA gene clusters and telomeric repeats during explosive genome repatterning in TATERILLUS X (Rodentia, Gerbillinae). Cytogenet Genome Res 2004; 103:94-103. [PMID: 15004471 DOI: 10.1159/000076296] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2003] [Accepted: 08/14/2003] [Indexed: 11/19/2022] Open
Abstract
A survey of 28S and 5S rRNA gene clusters, and telomeric repeats was performed using single and double FISH in the Taterillus genus (Rodentia, Muridae, Gerbillinae). Taterillus was previously demonstrated to have undergone a very recent and extensive chromosomal evolution. Our FISH results demonstrate that rRNA genes can vary in location and number irrespective of the phylogenetic relationships. Telomeric repeats were detected in pericentromeric and interstitial regions of several chromosomes, thus providing nonambiguous evolutionary footprints of Robertsonian and tandem translocation events. These footprints are discussed in reference to the molecular process of these karyotypical changes. Also, examples of colocation of rDNA clusters and telomeric repeats lend support to their possible involvement in nucleolus formation. Finally, the presence of rRNA genes, and the extensive amplification of telomeric repeats at specific loci within a double X-autosome translocated element which were not observed on the homologous Y1 and Y2, served as basis for an epigenomic hypothesis on X-autosome translocation viability in mammals.
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Affiliation(s)
- G Dobigny
- Laboratoire Origine, Structure et Evolution de la Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
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47
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Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics 2003; 1:30-40. [PMID: 15601531 PMCID: PMC3525001 DOI: 10.1186/1479-7364-1-1-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 08/19/2003] [Indexed: 11/10/2022] Open
Abstract
Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are presented in a first multispecies attempt using ordered mapping data to reconstruct the evolutionary exchanges that preceded modern placental mammal genomes.
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Affiliation(s)
- William J Murphy
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.
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48
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Abstract
The genomes of human, mouse, and rat have been sequenced. Now, as O'Brien and Murphy announce in their Perspective, the genome sequence derby is heating up with the addition of dog to the list (Kirkness et al.). As they explain, even though the coverage of the dog genome (1.5x) is lower than that of mouse (8x), there are many valuable insights to be gained from comparing the sequence of dog with those of mouse and human.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
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49
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Abstract
The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, Maryland 21702-1201, USA.
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