Browse > Article
http://dx.doi.org/10.5483/BMBRep.2013.46.6.185

Acceleration of X-chromosome gene order evolution in the cattle lineage  

Park, Woncheoul (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Oh, Hee-Seok (Department of Statistics, Seoul National University)
Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Publication Information
BMB Reports / v.46, no.6, 2013 , pp. 310-315 More about this Journal
Abstract
The gene order on the X chromosome of eutherians is generally highly conserved, although an increase in the rate of rearrangement has been reported in the rodent lineage. Conservation of the X chromosome is thought to be caused by selection related to maintenance of dosage compensation. However, we herein reveal that the cattle (Btau4.0) lineage has experienced a strong increase in the rate of X-chromosome rearrangement, much stronger than that previously reported for rodents. We also show that this increase is not matched by a similar increase on the autosomes and cannot be explained by assembly errors. Furthermore, we compared the difference in two cattle genome assemblies: Btau4.0 and Btau6.0 (Bos taurus UMD3.1). The results showed a discrepancy between Btau4.0 and Btau6.0 cattle assembly version data, and we believe that Btau6.0 cattle assembly version data are not more reliable than Btau4.0.
Keywords
Cattle; Eutheria; Evolution; Gene order; X chromosome;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Partipilo, G., D'Addabbo, P., Lacalandra, G. M., Liu, G. E. and Rocchi, M. (2011) Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. BMC Genomics 12, 639.   DOI
2 Heard, E. (2004) Recent advances in X-chromosome inactivation. Curr. Opin. Cell Biol. 16, 247-255.   DOI   ScienceOn
3 Raudsepp, T., Lee, E. J., Kata, S. R., Brinkmeyer, C., Mickelson, J. R., Skow, L. C., Womack, J. E. and Chowdhary, B. P. (2004) Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc. Natl. Acad. Sci. U.S.A. 101, 2386-2391.   DOI
4 Ross, M. T., Grafham, D. V., Coffey, A. J., Scherer, S., McLay, K., Muzny, D., Platzer, M., Howell, G. R., Burrows, C., Bird, C. P., Frankish, A., Lovell, F. L., Howe, K. L., Ashurst, J. L., Fulton, R. S., Sudbrak, R., Wen, G., Jones, M. C., Hurles, M. E., Andrews, T. D., Scott, C. E., Searle, S., Ramser, J., Whittaker, A., Deadman, R., Carter, N. P., Hunt, S. E., Chen, R., Cree, A., Gunaratne, P., Havlak, P., Hodgson, A., Metzker, M. L., Richards, S., Scott, G., Steffen, D., Sodergren, E., Wheeler, D. A., Worley, K. C., Ainscough, R., Ambrose, K. D., Ansari-Lari, M. A., Aradhya, S., Ashwell, R. I., Babbage, A. K., Bagguley, C. L., Ballabio, A., Banerjee, R., Barker, G. E., Barlow, K. F., Barrett, I. P., Bates, K. N., Beare, D. M., Beasley, H., Beasley, O., Beck, A., Bethel, G., Blechschmidt, K., Brady, N., Bray-Allen, S., Bridgeman, A. M., Brown, A. J., Brown, M. J., Bonnin, D., Bruford, E. A., Buhay, C., Burch, P., Burford, D., Burgess, J., Burrill, W., Burton, J., Bye, J. M., Carder, C., Carrel, L., Chako, J., Chapman, J. C., Chavez, D., Chen, E., Chen, G., Chen, Y., Chen, Z., Chinault, C., Ciccodicola, A., Clark, S. Y., Clarke, G., Clee, C. M., Clegg, S., Clerc-Blankenburg, K., Clifford, K., Cobley, V., Cole, C. G., Conquer, J. S., Corby, N., Connor, R. E., David, R., Davies, J., Davis, C., Davis, J., Delgado, O., Deshazo, D., Dhami, P., Ding, Y., Dinh, H., Dodsworth, S., Draper, H., Dugan-Rocha, S., Dunham, A., Dunn, M., Durbin, K. J., Dutta, I., Eades, T., Ellwood, M., Emery-Cohen, A., Errington, H., Evans, K. L., Faulkner, L., Francis, F., Frankland, J., Fraser, A. E., Galgoczy, P., Gilbert, J., Gill, R., Glockner, G., Gregory, S. G., Gribble, S., Griffiths, C., Grocock, R., Gu, Y., Gwilliam, R., Hamilton, C., Hart, E. A., Hawes, A., Heath, P. D., Heitmann, K., Hennig, S., Hernandez, J., Hinzmann, B., Ho, S., Hoffs, M., Howden, P. J., Huckle, E. J., Hume, J., Hunt, P. J., Hunt, A. R., Isherwood, J., Jacob, L., Johnson, D., Jones, S., de Jong, P. J., Joseph, S. S., Keenan, S., Kelly, S., Kershaw, J. K., Khan, Z., Kioschis, P., Klages, S., Knights, A. J., Kosiura, A., Kovar-Smith, C., Laird, G. K., Langford, C., Lawlor, S., Leversha, M., Lewis, L., Liu, W., Lloyd, C., Lloyd, D. M., Loulseged, H., Loveland, J. E., Lovell, J. D., Lozado, R., Lu, J., Lyne, R., Ma, J., Maheshwari, M., Matthews, L. H., McDowall, J., McLaren, S., McMurray, A., Meidl, P., Meitinger, T., Milne, S., Miner, G., Mistry, S. L., Morgan, M., Morris, S., Muller, I., Mullikin, J. C., Nguyen, N., Nordsiek, G., Nyakatura, G., O'Dell, C. N., Okwuonu, G., Palmer, S., Pandian, R., Parker, D., Parrish, J., Pasternak, S., Patel, D., Pearce, A. V., Pearson, D. M., Pelan, S. E., Perez, L., Porter, K. M., Ramsey, Y., Reichwald, K., Rhodes, S., Ridler, K. A., Schlessinger, D., Schueler, M. G., Sehra, H. K., Shaw-Smith, C., Shen, H., Sheridan, E. M., Shownkeen, R., Skuce, C. D., Smith, M. L., Sotheran, E. C., Steingruber, H. E., Steward, C. A., Storey, R., Swann, R. M., Swarbreck, D., Tabor, P. E., Taudien, S., Taylor, T., Teague, B., Thomas, K., Thorpe A., Timms, K., Tracey, A., Trevanion, S., Tromans, A. C., d'Urso, M., Verduzco, D., Villasana, D., Waldron, L., Wall, M., Wang, Q., Warren, J., Warry, G. L., Wei, X., West, A., Whitehead, S. L., Whiteley, M. N., Wilkinson, J. E., Willey, D. L., Williams, G., Williams, L., Williamson, A., Williamson, H., Wilming, L., Woodmansey, R. L., Wray, P. W., Yen, J., Zhang, J., Zhou, J., Zoghbi, H., Zorilla, S., Buck, D., Reinhardt, R., Poustka, A., Rosenthal, A., Lehrach, H., Meindl, A., Minx, P. J., Hillier, L. W., Willard, H. F., Wilson, R. K., Waterston, R. H., Rice, C. M., Vaudin, M., Coulson, A., Nelson, D. L., Weinstock, G., Sulston, J. E., Durbin, R., Hubbard, T., Gibbs, R. A., Beck, S., Rogers, J. and Bentley, D. R. (2005) The DNA sequence of the human X chromosome. Nature 434, 325-337.   DOI   ScienceOn
5 Arias, J. A., Keehan, M., Fisher, P., Coppieters, W. and Spelman, R. (2009) A high density linkage map of the bovine genome. BMC Genet. 10, 18.
6 Sims, G. E., Jun, S. R., Wu, G. A. and Kim, S. H. (2009) Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc. Natl. Acad. Sci. U.S.A. 106, 17077-17082.   DOI   ScienceOn
7 Keightley, P. D. and Eyre-Walker, A. (2000) Deleterious mutations and the evolution of sex. Science 290, 331-333.   DOI   ScienceOn
8 Li, W. H., Gouy, M., Sharp, P. M., O'HUigin, C. and Yang, Y. W. (1990) Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks. Proc. Natl. Acad. Sci. U.S.A. 87, 6703-6707.   DOI
9 Hannenhalli, S. and Pevzner, P. A. (1999) Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM 46, 1-27.   DOI   ScienceOn
10 Tesler, G. (2002) GRIMM: genome rearrangements web server. Bioinformatics 18, 492-493.   DOI   ScienceOn
11 Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees.Mol. Biol. Evol. 4, 406-425.
12 Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J. and Marra, M. A. (2009) Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.   DOI   ScienceOn
13 Frith, M. C., Hamada, M. and Horton, P. (2010) Parameters for accurate genome alignment. BMC Bioinformatics 11, 80.   DOI   ScienceOn
14 Lyon, M. F. (2003) The Lyon and the LINE hypothesis. Semin. Cell Dev. Biol. 14, 313-318.   DOI   ScienceOn
15 Penny, G. D., Kay, G. F., Sheardown, S. A., Rastan, S. and Brockdorff, N. (1996) Requirement for Xist in X chromosome inactivation. Nature 379, 131-137.   DOI   ScienceOn
16 Gartler, S. M. and Riggs, A. D. (1983) Mammalian X-chromosome inactivation. Annu. Rev. Genet. 17, 155-190.   DOI   ScienceOn
17 Lyon, M. F. (1998) X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell. Genet. 80, 133-137.   DOI   ScienceOn
18 Ohno, S. (1973) Ancient linkage groups and frozen accidents. Nature 244, 259-262.   DOI   ScienceOn
19 Graves, J. A., Disteche, C. M. and Toder, R. (1998) Gene dosage in the evolution and function of mammalian sex chromosomes. Cytogenet. Cell Genet. 80, 94-103.   DOI   ScienceOn
20 Graves, J. A. and Watson, J. M. (1991) Mammalian sex chromosomes: evolution of organization and function. Chromosoma 101, 63-68.   DOI
21 Delgado, C. L., Waters, P. D., Gilbert, C., Robinson, T. J. and Graves, J. A. (2009) Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years. Chromosome Res. 17, 917-926.   DOI
22 Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S. E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M. R., Brown, D. G., Brown, S. D., Bult, C., Burton, J., Butler, J., Campbell, R. D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A. T., Church, D. M., Clamp, M., Clee, C., Collins, F. S., Cook, L. L., Copley, R. R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K. D., Deri, J., Dermitzakis, E. T., Dewey, C., Dickens, N. J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D. M., Eddy, S. R., Elnitski, L., Emes, R. D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G. A., Flicek, P., Foley, K., Frankel, W. N., Fulton, L. A., Fulton, R. S., Furey, T. S., Gage, D., Gibbs, R. A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T. A., Green, E. D., Gregory, S., Guigo, R., Guyer, M., Hardison, R. C., Haussler, D., Hayashizaki, Y., Hillier, L. W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D. B., Johnson, L. S., Jones, M., Jones, T. A., Joy, A., Kamal, M., Karlsson, E. K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W. J., Kirby, A., Kolbe, D. L., Korf, I., Kucherlapati, R. S., Kulbokas, E. J., Kulp, D., Landers, T., Leger, J. P., Leonard, S., Letunic, I., Levine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D. R., Mardis, E. R., Matthews, L., Mauceli, E., Mayer, J. H., McCarthy, M., McCombie, W. R., McLaren, S., McLay, K., McPherson, J. D., Meldrim, J., Meredith, B., Mesirov, J. P., Miller, W., Miner, T. L., Mongin, E., Montgomery, K. T., Morgan, M., Mott, R., Mullikin, J. C., Muzny, D. M., Nash, W. E., Nelson, J. O., Nhan, M. N., Nicol, R., Ning, Z., Nusbaum, C., O'Connor, M. J., Okazaki, Y., Oliver, K., Overton-Larty, E., Pachter, L., Parra, G., Pepin, K. H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C. S., Poliakov, A., Ponce, T. C., Ponting, C. P., Potter, S., Quail, M., Reymond, A., Roe, B. A., Roskin, K. M., Rubin, E. M., Rust, A. G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M. S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J. B., Slater, G., Smit, A., Smith, D. R., Spencer, B., Stabenau, A., Stange-Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta-Vidal, A., Vinson, J. P., Von Niederhausern, A. C., Wade, C. M., Wall, M., Weber, R. J., Weiss, R. B., Wendl, M. C., West, A. P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R. K., Winter, E., Worley, K. C., Wyman, D., Yang, S., Yang, S. P., Zdobnov, E. M., Zody, M. C. and Lander, E. S. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.   DOI   ScienceOn
23 Sandstedt, S. A. and Tucker, P. K. (2004) Evolutionary strata on the mouse X chromosome correspond to strata on the human X chromosome. Genome Res. 14, 267-272.   DOI   ScienceOn
24 Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M. L., Goh, G., Seabury, C. M., Brinkmeyer-Langford, C., Lee, E. J., Agarwala, R., Stallknecht-Rice, E., Schaffer, A. A., Skow, L. C., Tozaki, T., Yasue, H., Penedo, M. C., Lyons, L. A., Khazanehdari, K. A., Binns, M. M., MacLeod, J. N., Distl, O., Guerin, G., Leeb, T., Mickelson, J. R. and Chowdhary, B. P. (2008) A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet. Genome Res. 122, 28-36.   DOI   ScienceOn
25 Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P. and Sonstegard, T. S. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10, R42.   DOI   ScienceOn
26 Amaral, M. E., Kata, S. R. and Womack, J. E. (2002) A radiation hybrid map of bovine X chromosome (BTAX). Mamm. Genome 13, 268-271.   DOI   ScienceOn
27 Fadista, J. and Bendixen, C. (2012) Genomic position mapping discrepancies of commercial SNP chips. PloS One 7, e31025.   DOI