A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae

Genomics

Volumn 93, Issue 4, 2009, Pages 299-304

  Davis, Brian W ^a   Raudsepp, Terje ^a   Pearks Wilkerson, Alison J ^a   Agarwala, Richa ^b   Schäffer, Alejandro A ^b   Houck, Marlys ^c   Chowdhary, Bhanu P ^a   Murphy, William J ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c INSTITUTE FOR CONSERVATION RESEARCH   (United States)

Author keywords

Chromosome rearrangement; Comparative mapping; Domestic cat; Felidae; FISH mapping; Radiation hybrid map; Synteny

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CAT; CHROMOSOME REARRANGEMENT; FLUORESCENCE IN SITU HYBRIDIZATION; GENE MAPPING; GENETIC CONSERVATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RADIATION HYBRID MAPPING; SYNTENY;

FELIDAE; FELIS CATUS; LEPTAILURUS SERVAL; PANTHERA; PROFELIS; UNCIA UNCIA;

EID: 61849170302     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2008.09.010     Document Type: Article

References (32)

1. Menotti-Raymond M., David V.A., Agarwala R., Schäffer A.A., Stephens R., O'Brien S.J., and Murphy W.J. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenet. Genome Res. 102 (2003) 272-276
2. Menotti-Raymond M., David V.A., Roelke M.E., Chen Z.Q., Menotti K.A., Sun S., Schäffer A.A., Tomlin J.F., Agarwala R., O'Brien S.J., and Murphy W.J. Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J. Heredity 94 (2003) 95-106
3. Murphy W.J., Davis B., David V.A., Agarwala R., Schäffer A.A., Pearks Wilkerson A.J., Neelam B., O'Brien S.J., and 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 89 (2007) 189-196
4. Murphy W.J., Sun S., Chen Z., Yuhki N., Hirschmann D., Menotti-Raymond M., and O'Brien S.J. A radiation hybrid map of the cat genome: implications for comparative mapping. Genome Res. 10 (2000) 691-702
5. Kehler J.S., David V.A., Schäffer A.A., Bajema K., Eizirik E., Ryugo D.K., Hannah S.S., O'Brien S.J., and Menotti-Raymond M. Four independent mutations in the feline fibroblast growth factor 5 gene determine the long-haired phenotype in domestic cats. J. Heredity 98 (2007) 555-566
6. Lyons L.A., Imes D.L., Rah H.C., and Grahn R.A. Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus). Anim. Genet. 36 (2005) 119-126
7. Schmidt-Küntzel A., Eizirik E., O'Brien S.J., and Menotti-Raymond M. Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of the albino and brown loci. J. Heredity 96 (2005) 289-301
8. Lyons L.A., Biller D.S., Erdman C.A., Lipinski M.J., Young A.E., Roe B.A., Qin B., and Grahn R.A. Feline polycystic kidney disease mutation identified in PKD1. J. Am. Soc. Nephrol. 15 (2004) 2548-2555
9. Meurs K.M., Sanchez X., David R.M., Bowles N.E., Towbin J.A., Reiser P.J., Kittleson J.A., Munro M.J., Dryburgh K., Macdonald K.A., and Kittleson M.D. A cardiac myosin binding protein C mutation in the Maine Coon cat with familial hypertrophic cardiomyopathy. Hum. Mol. Genet. 14 (2005) 3587-3593
10. Fyfe J.C., Menotti-Raymond M., David V.A., Brichta L., Schäffer A.A., Agarwala R., Murphy W.J., Wedemeyer W.J., Gregory B.L., Buzzell B.G., Drummond M.C., Wirth B., and O'Brien S.J. An ∼ 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res. 16 (2006) 1084-1090
11. Menotti-Raymond M., David V.A., Schäffer A.A., Stephens R., Wells D., Kumar-Singh R., O'Brien S.J., and Narfström K. Mutation in CEP290 discovered for cat model of human retinal degeneration. J. Heredity 98 (2007) 211-220
12. Hitte C., Madeoy J., Kirkness E.F., Priat C., Lorentzen T.D., Senger F., Thomas D., Derrien T., Ramirez C., Scott C., Evanno G., Pullar B., Cadieu E., Oza V., Lourgant K., Jaffe D.B., Tacher S., Dreano S., Berkova N., André C., Deloukas P., Fraser C., Lindblad-Toh K., Ostrander E.A., and Galibert F. Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping. Nat. Rev. Genet. 6 (2005) 643-648
13. Murphy W.J., Larkin D.M., Everts-van der Wind A., Bourque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers S.N., Milan D., Ostrander E.A., Pape G., Parker H.G., Raudsepp T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., O'Brien S J., Pevzner P.A., and Lewin H.A. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309 (2005) 613-617
14. Pontius J.U., Mullikin J.C., Smith D.R., Lindblad-Toh K., Gnerre S., Clamp M., Chang J., Stephens R., Neelam B., Volfovsky N., Schäffer A.A., Agarwala R., Narfstrom K., Murphy W.J., Giger U., Roca A.L., Antunes A., Menotti-Raymond M., Yuhki N., Pecon-Slattery J., Johnson W.E., Bourque G., Tesler G., and O'Brien S.J. Initial sequence and comparative analysis of the cat genome. Genome Res. 17 (2007) 1675-1689
15. M. Menotti-Raymond, V.A. David, A.A. Schäffer, J.F. Tomlin, E. Eizirik, C. Philip, D. Wells, J.U. Pontius, S.S. Hannah, S.J. O'Brien, A third-generation autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics (in press).
16. Derrien T., André C., Galibert F., and Hitte C. AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics 23 (2007) 498-499
17. Everts-van der Wind A., Larkin D.M., Green C.A., Elliott J.S., Olmstead C.A., Chiu R., Schein J.E., Marra M.A., Womack J.E., and Lewin H.A. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 18526-18531
18. Nash W.G., Menninger J.C., Wienberg J., Padilla-Nash H.M., and O'Brien S.J. The pattern of phylogenomic evolution of the Canidae. Cytogenet. Cell Genet. 95 (2001) 210-224
19. Yang F., Graphodatsky A.S., O'Brien P.C., Colabella A., Solanky N., Squire M., Sargan D.R., and Ferguson-Smith M.A. Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human. Chromosome Res. 8 (2000) 393-404
20. Graphodatsky A.S., Perelman P.L., Sokolovskaya N.V., Beklemisheva V.R., Serdukova N.A., Dobigny G., O'Brien S.J., Ferguson-Smith M.A., and Yang F. Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting. Chromosome Res. 16 (2008) 129-143
21. Johnson W.E., Eizirik E., Pecon-Slattery J., Murphy W.J., Antunes A., Teeling E., and O'Brien S.J. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311 (2006) 73-77
22. Wurster-Hill D.H., and Centerwall W.R. The interrelationships of chromosome banding patterns in canids, mustelids, hyena, and felids. Cytogenet. Cell Genet. 34 (1982) 178-192
23. Stanyon R., Rocchi M., Capozzi O., Roberto R., Misceo D., Ventura M., Cardone M.F., Bigoni F., and Archidiacono N. Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres. Chromosome Res. 16 (2008) 17-39
24. E. Eizirik, W.J. Murphy, Carnivora. in: S.B. Hedges, S. Kumar, S., (Ed.), Assembling the Timetree of Life, Oxford University Press, Oxford, in press.
25. Rozen S., and Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132 (2000) 365-386
26. Agarwala R., Applegate D.L., Maglott D., Schuler G.D., and Schäffer A.A. A fast and scalable radiation hybrid map construction and integration strategy. Genome Res. 10 (2000) 350-364
27. Schäffer A.A., Rice E.S., Cook W., and Agarwala R. rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinformatics 23 (2007) 1156-1158
28. Applegate D.L. The Traveling Salesman Problem: A Computational Study (2006), Princeton University Press, Princeton
29. Larkin D.M., Everts-van der Wind A., Rebeiz M., Schweitzer P.A., Bachman S., Green C., Wright C.L., Campos E.J., Benson L.D., Edwards J., Liu L., Osoegawa K., Womack J.E., de Jong P.J., and Lewin H.A. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res. 13 (2003) 1966-1972
30. O'Brien S.J., and Nash W.G. Genetic mapping in mammals: chromosome map of domestic cat. Science 216 (1982) 257-265
31. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12 (2002) 656-664
32. Zhang Z., Schwartz S., Wagner L., and Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7 (2000) 203-214