Microsatellite accumulation on the Y chromosome in Silene latifolia

Genome

Volumn 51, Issue 5, 2008, Pages 350-356

  Kubat, Zdenek ^a   Hobza, Roman ^a   Vyskot, Boris ^a   Kejnovsky, Eduard ^a  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

Microsatellites; Plant sex chromosomes; Silene latifolia

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; METAPHASE; PLANT CHROMOSOME; SILENE;

CHROMOSOMES, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; METAPHASE; MICROSATELLITE REPEATS; SILENE;

MAMMALIA; SILENE; SILENE LATIFOLIA;

EID: 44449104985     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G08-024     Document Type: Article

References (53)

1. Bachtrog, D. 2006a. A dynamic view of sex chromosome evolution. Curr. Opin. Genet. Dev. 16: 578-585. doi:10.1016/j.gde.2006.10.007. PMID:17055249.
2. Bachtrog, D. 2006b. Expression profile of a degenerating neo-Y chromosome in Drosophila. Curr. Biol. 16: 1694-1699. doi:10.1016/j.cub.2006.07.053. PMID:16950105.
3. Bacolla, A., and Wells, R.D. 2004. Non-B DNA conformations, genomic rearrangements, and human disease. J. Biol. Chem. 279: 47411-47414. doi:10.1074/jbc.R400028200. PMID:15326170.
4. Bergero, R., Forrest, A., Kamau, E., and Charlesworth, D. 2007. Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: evidence from new sex-linked genes. Genetics, 175: 1945-1954. doi:10.1534/genetics.106.070110. PMID:17287532.
5. Buzek, J., Koutnikova, H., Houben, A., Riha, K., Janousek, B., Siroky, J., et al. 1997. Isolation and charecterization of X chromosome-derived DNA sequences from a dioecious plant Melandrium album. Chromosome Res. 5: 57-65. doi:10.1023/A:1011693603279. PMID:9088644.
6. Charlesworth, B., and Charlesworth, D. 2000. The degeneration of Y chromosomes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355: 1563-1572. doi:10.1098/rstb.2000.0717. PMID:11127901.
7. Charlesworth, B., Langley, C.H., and Stephan, W. 1986. The evolution of restricted recombination and the accumulation of repeated DNA sequences. Genetics, 112: 947-962. PMID:3957013.
8. Charlesworth, B., Sniegowski, P., and Stephan, W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature (London), 371: 215-220. doi:10.1038/371215a0. PMID:8078581.
9. Charlesworth, D., Charlesworth, B., and Marais, G. 2005. Steps in the evolution of heteromorphic sex chromosomes. Heredity, 95: 118-128. doi:10.1038/sj.hdy.6800697. PMID:15931241.
10. Ciupercescu, D.D. 1990. Karyotyping Melandrium album, a dioecious plant with heteromorphic sex chromosomes. Genome, 33: 556-562. doi:10.1139/g90-082.
11. Cuadrado, A., and Schwarzacher, T. 1998. The chromosomal organization of simple sequence repeats in wheat and rye genomes. Chromosoma, 107: 587-594. doi:10.1007/s004120050345. PMID:9933412.
12. Drummond, D.A., Bloom, J.D., Adami, C., Wilke, C.O., and Arnold, F.H. 2005. Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. U.S.A. 102: 14338-14343. doi:10.1073/pnas.0504070102. PMID:16176987.
13. Ellegren, H. 2004. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5: 435-445. doi:10.1038/nrg1348. PMID:15153996.
14. Guttman, D.S., and Charlesworth, D. 1998. An X-linked gene has a degenerate Y-linked homologue in the dioecious plant Silene latifolia. Nature (London), 393: 263-266. doi:10.1038/30492. PMID:9607762.
15. Hobza, R., Lengerova, M., Cernohorska, H., Rubes, J., and Vyskot, B. 2004. FAST-FISH with laser beam microdissected DOP-PCR probe distinguishes the sex chromosomes of Silene latifolia. Chromosome Res. 12: 245-250. doi:10.1023/B:CHRO.0000021929.97208.1c. PMID:15125638.
16. Hobza, R., Lengerova, M., Svoboda, J., Kubekova, H., Kejnovsky, E., and Vyskot, B. 2006. An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution. Chromosoma, 115: 376-382. doi:10.1007/s00412-006-0065-5. PMID:16612641.
17. Hobza, R., Kejnovsky, E., Vyskot, B., and Widmer, A. 2007. The role of chromosomal rearrangements in the evolution of Silene latifolia sex chromosomes. Mol. Genet. Genomics, 278: 633-638. doi:10.1007/s00438-007- 0279-0.
18. Jakupciak, J.P., and Wells, R.D. 2000. Genetic instabilities of triplet repeat sequences by recombination. IUBMB Life, 50: 355-359. PMID:11327307.
19. Kejnovská, I., Kypr, J., and Vorlíčková, M. 2003. Circular dichroism spectroscopy of conformers of (guanine plus adenine) repeat strands of DNA. Chirality, 15: 584-592. doi:10.1002/chir.10249. PMID:12840822.
20. Kejnovsky, E., Kubat, Z., Hobza, R., Lengerova, M., Sato, S., Tabata, S., et al. 2006a. Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifolia. Genetica, 128: 167-175. doi:10.1007/s10709-005-5701-0. PMID:17028949.
21. Kejnovsky, E., Kubat, Z., Macas, J., Hobza, R., Mracek, J., and Vyskot, B. 2006b. Retand: a novel family of gypsy-like retrotransposons harbouring an amplified tandem repeat. Mol. Genet. Genomics, 276: 254-263. doi:10.1007/s00438-006-0140-x. PMID:16826419.
22. Kejnovsky, E., Hobza, R., Kubat, Z., Widmer, A., Marais, G.A.B., and Vyskot, B. 2007. High intrachromosomal similarity of retrotransposon long terminal repeats: evidence for homogenization by gene conversion on plant sex chromosomes? Gene, 390: 92-97. doi:10.1016/j.gene.2006.10.007. PMID:17134852.
23. Lahn, B.T., and Page, D.C. 1999. Four evolutionary strata on the human X chromosome. Science (Washington, D.C.), 286: 964-967. doi:10.1126/science.286.5441.964. PMID:10542153.
24. Lengerova, M., Kejnovsky, E., Hobza, R., Macas, J., Grant, S.R., and Vyskot, B. 2004. Multicolor FISH mapping of the dioecious model plant, Silene latifolia. Theor. Appl. Genet. 108: 1193-1199. doi:10.1007/s00122- 003-1568-6. PMID:14727034.
25. Levinson, G., and Gutman, G.A. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203-221. PMID:3328815.
26. Liu, Z., Moore, P.H., Ma, H., Ackerman, C.M., Ragiba, M., Yu, Q., et al. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature (London), 427: 348-352. doi:10.1038/nature02228. PMID:14737167.
27. Marais, G., Nicolas, M., Bergero, R., Chambrier, P., Kejnovsky, E., Mone'ger, F., et al. 2008. Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia. Curr. Biol. 18. doi:10.1016/j.cub.2008.03.023.
28. Matsunaga, S. 2006. Sex chromosome-linked genes in plants. Genes Genet. Syst. 81: 219-226. doi:10.1266/ggs.81.219. PMID:17038793.
29. Matsunaga, S., Isono, E., Kejnovsky, E., Vyskot, B., Dolezel, J., Kawano, S., and Charlesworth, D. 2003. Duplicative transfer of a MADS box gene to a plant Y chromosome. Mol. Biol. Evol. 20: 1062-1069. doi:10.1093/molbev/ msg114. PMID:12716981.
30. Morgante, M., Hanafey, M., and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200. doi:10.1038/ng822. PMID: 11799393.
31. Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C., Shimizu, A., et al. 2002. A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc. Natl. Acad. Sci. U.S.A. 99: 11778-11783. doi:10.1073/pnas.182314699. PMID:12193652.
32. Napierala, M., Dere, R., Vetcher, A., and Wells, R.D. 2004. Structure-dependent recombination hot spot activity of GAA·TTC sequences from intron 1 of the Friedreich's ataxia gene. J. Biol. Chem. 279: 6444-6454. doi:10.1074/jbc.M309596200. PMID:14625270.
33. Nichol, K., and Pearson, C.E. 2002. CpG methylation modifies the genetic stability of cloned repeat sequences. Genome Res. 12: 1246-1256. doi:10.1101/gr.74502. PMID:12176932.
34. Nicolas, M., Marais, G., Hykelova, V., Janousek, B., Laporte, V., Vyskot, B., et al. 2005. A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. PLoS Biol. 3: e4. doi:10.1371/journal.pbio.0030004.
35. Okada, S., Sone, T., Fujisawa, M., Nakayama, S., Takenaka, M., Ishizaki, K., et al. 2001. The Y chromosome in the liverwort Marchantia polymorpha has accumulated unique repeat sequences harboring a male-specific gene. Proc. Natl. Acad. Sci. U.S.A. 98: 9454-9459. doi:10.1073/pnas.171304798. PMID:11481501.
36. Peichel, C.L., Ross, J.A., Matson, C.K., Dickson, M., Grimwood, J., Schmutz, J., et al. 2004. The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr. Biol. 14: 1416-1424. doi:10.1016/j.cub.2004.08.030. PMID:15324658.
37. Sakamoto, K., Akiyama, Y., Fukui, K., Kamada, H., and Satoh, S. 1998. Characterization, genome sizes and morphology of sex chromosome in hemp (Cannabis sativa L.). Cytologia (Tokyo), 63: 459-464.
38. Sakamoto, N., Chastain, P.D., Parniewski, P., Ohshima, K., Pandolfo, M., Griffith, J.D., and Wells, R.D. 1999. Sticky DNA: self-association properties of long GAA·TTC repeats in R·R·Y triplex structures from Friedreich's ataxia. Mol. Cell, 3: 465-475. doi:10.1016/S1097-2765(00) 80474-8. PMID:10230399.
39. Sakamoto, K., Ohmido, N., Fukui, K., Kamada, H., and Satoh, S. 2000. Site-specific accumulation of LINE-like retrotransposon in a sex chromosome of the dioecious plant Cannabis sativa. Plant Mol. Biol. 44: 723-732. doi:10.1023/A:1026574405717. PMID:11202435.
40. Sakamoto, N., Ohshima, K., Montermini, L., Pandolfo, M., and Wells, R.D. 2001. Sticky DNA, a self-associated complex formed at long GAA·TTC repeats in intron 1 of the Frataxin gene, inhibits transcription. J. Biol. Chem. 276: 27171-27177. doi:10.1074/jbc.M101879200. PMID:11340071.
41. Schlotterer, C. 2000. Evolutionary dynamics of microsatellite DNA. Chromosoma, 109: 365-371. doi:10.1007/s004120000089. PMID:11072791.
42. Schmidt, T., and Heslop-Harrison, J.S. 1996. The physical and genomic organization of microsatellites in sugar beet. Proc. Natl. Acad. Sci. U.S.A. 93: 8761-8765. doi:10.1073/pnas.93.16.8761. PMID:8710945.
43. Shibata, F., Hizume, M., and Kuroki, Y. 1999. Chromosome painting of Y chromosomes and isolation of a Y chromosome-specific repetitive sequence in the dioecious plant Rumex acetosa. Chromosoma, 108: 266-270. doi:10.1007/s004120050377. PMID:10460415.
44. Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P.J., Cordum, H.S., Hillier, L., Brown, L.G.et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature (London), 423: 825-837. doi:10.1038/nature01722. PMID:12815422.
45. Steinemann, S., and Steinemann, M. 2005. Y chromosomes: born to be destroyed. Bioessays, 27: 1076-1083. doi:10.1002/bies.20288. PMID:16163733.
46. Stephan, W., and Cho, S. 1994. Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. Genetics, 136: 333-341. PMID:8138169.
47. Subramanian, S., Mishra, R.K., and Singh, L. 2003. Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 4: R13. doi:10.1186/gb-2003-4-2-r13. PMID:12620123.
48. Tero, N., Neumeier, H., Gudavalli, R., and Schlotterer, C. 2006. Silene tatarica microsatellites are frequently located in repetitive DNA. J. Evol. Biol. 19: 1612-1619. doi:10.1111/j.1420-9101. 2006.01118.x. PMID:16910990.
49. Timmis, J.N., Ayliffe, M.A., Huang, C.Y., and Martin, W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5: 123-135. doi:10.1038/nrg1271. PMID:14735123.
50. Vyskot, B., and Hobza, R. 2004. Gender in plants: sex chromosomes are emerging from the fog. Trends Genet. 20: 432-438. doi:10.1016/j.tig.2004. 06.006. PMID:15313552.
51. Vyskot, B., Siroky, J., Hladilova, R., Belyaev, N., and Turner, B.M. 1999. Euchromatic domains in plant chromosomes as revealed by H4 histone acetylation and early DNA replication. Genome, 42: 343-350. doi:10.1139/gen-42-2-343. PMID:10231965.
52. Wells, R.D., Dere, R., Hebert, M.L., Napierala, M., and Son, L.S. 2005. Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Res. 33: 3785-3798. doi:10.1093/nar/gki697. PMID:16006624.
53. Zluvova, J., Janousek, B., Negrutiu, I., and Vyskot, B. 2005. Comparison of the X and Y chromosome organization in Silene latifolia. Genetics, 170: 1431-1434. doi:10.1534/genetics.105.040444. PMID:15879508.