Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: Evidence from new sex-linked genes

Genetics

Volumn 175, Issue 4, 2007, Pages 1945-1954

  Bergero, Roberta ^a   Forrest, Alan ^a   Kamau, Esther ^a   Charlesworth, Deborah ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; GENE IDENTIFICATION; GENE MAPPING; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC VARIABILITY; INTRON; MALE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; SEGREGATION ANALYSIS; SEQUENCE ANALYSIS; SEX CHROMOSOME; SEX LINKAGE; SILENE; SILENE LATIFOLIA; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; Y CHROMOSOME;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC MARKERS; INTRONS; LINKAGE (GENETICS); MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SILENE; VARIATION (GENETICS);

SILENE LATIFOLIA;

EID: 34248998839     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.070110     Document Type: Article

References (55)

1. ATANASSOV, I., C. DELICHERE, D. A. FILATOV, D. CHARLESWORTH, I. NEGRUTIU et al., 2001 Analysis and evolution of two functional Y-linked loci in a plant sex chromosome system. Mol. Biol. Evol. 18: 2162-2168.
2. BACHTROG, D., 2003 Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics 165: 1221-1232.
3. BACHTROG, D., 2004 Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda. Nat. Genet. 36: 518-522.
4. BRADLEY, R. D., and D. M. HILLIS, 1997 Recombinant DNA sequences generated by PCR amplification. Mol. Biol. Evol. 14: 592-593.
5. CARVALHO, A. B., 2002 Origin and evolution of the Drosophila Y chromosome. Curr. Opin. Genet. Dev. 12: 664-668.
6. COSTICH, D. E., T. R. MEAGHER and E. J. YURKOW, 1991 A rapid means of sex identification in Silene latifolia by use of flow cytometry. Plant Mol. Biol. Rep. 9: 359-370.
7. DELICHERE, C., J. VEUSKENS, M. HERNOULD, N. BARBACAR, A. MOURAS et al., 1999 SlY1, the first active gene cloned from a plant Y chromosome, encodes a WD-repeat protein. EMBO J. 18: 4169-4179.
8. DI STILIO, V. S., R. V. KESSELI and D. L. MULCAHY, 1998 A pseudoautosomal random amplified polymorphic DNA marker for the sex chromosomes of Silene dioica. Genetics 149: 2057-2062.
9. DONNISON, I. S., and S. R. GRANT, 1999 Male sex-specific DNA in Silene latifolia and other dioecious plant species, pp. 73-87 in Sex Determination in Plants, edited by C. C. AINSWORTH. BIOS, Oxford.
10. FELTUS, F. A., H. P. SINGH, H. C. LOHITHASWA, S. R. SCHULZE, T. D. SILVA et al., 2006 A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol. 140: 1183-1191.
11. FILATOV, D. A., 2005a Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes. Genetics 170: 975-979.
12. FILATOV, D. A., 2005b Isolation of genes from plant Y chromosomes. Methods Enzymol. 395: 418-442.
13. FILATOV, D. A., 2005c Substitution rates in a new Silene latifolia sex-linked gene, SlssX/Y. Mol. Biol. Evol. 22: 402-408.
14. GAO, L. Z., and H. INNAN, 2004 Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
15. GILLESPIE, J., 1991 The Causes of Molecular Evolution. Oxford University Press, Oxford.
16. GUTTMAN, D. S., and D. CHARLESWORTH, 1998 An X-linked gene with a degenerate Y-linked homologue in a dioecious plant. Nature 393: 263-266.
17. INADA, D. C., A. BASHIR, C. LEE, B. C. THOMAS, C. KO et al., 2003 Conserved noncoding sequences in the grasses. Genome Res. 13: 2030-2041.
18. KEJNOVSKY, E., J. VRANA, S. MATSUNAGA, P. SOUCEK, J. SIROKY et al., 2001 Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes. Genetics 158: 1269-1277.
19. KEJNOVSKY, E., Z. KUBAT, R. HOBZA, M. LENGEROVA, H. SATO et al., 2006 Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifolia. Genetica 128: 167-175.
20. KONDO, M., I. NANDA, U. HORNUNG, M. SCHMID and M. SCHARTL, 2004 Evolutionary origin of the medaka Y chromosome. Curr. Biol. 14: 1664-1669.
21. LAHN, B. T., and D. C. PAGE, 1999 Four evolutionary strata on the human X chromosome. Science 286: 964-967.
22. LAWSON-HANDLEY, L. J., H. CEPLITIS and and H. ELLEGREN, 2004 Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics 167: 367-376.
23. LEBEL-HARDENACK, S., E. HAUSER, T. F. LAW, J. SCHMID and S. R. GRANT, 2002 Mapping of sex determination loci on the white campion (Silene latifolia) Y chromosome using amplified fragment length polymorphism. Genetics 160: 717-725.
24. LENGEROVA, M., E. KEJNOVSKY, R. HOBZA, J. MACAS, S. R. GRANT et al., 2004 Multicolor FISH mapping of the dioecious model plant, Silene latifolia. Theor. Appl. Genet. 108: 1193-1199.
25. LIU, F., L. ZHANG and D. CHARLESWORTH, 1998 Genetic diversity in Leavenworthia populations with different inbreeding levels. Proc. Biol. Sci. 265: 293-301.
26. LIU, F., D. CHARLESWORTH and M. KREITMAN, 1999 The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics 151: 343-357.
27. LIU, Z., P. H. MOORE, H. MA, C. M. ACKERMAN, M. RAGIBA et al., 2004 A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348-352.
28. MA, H., P. H. MOORE, Z. LIU, M. S. KIM, Q. YU et al., 2004 High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166: 419-436.
29. MARCHUK, D., M. DRUMM, A. SAULINO and F. S. COLLINS, 1991 Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res. 19: 1154.
30. MATSUNAGA, S., E. ISONO, E. KEJNOVSKY, B. VYSKOT, J. DOLEZEL et al., 2003 Duplicative transfer of a MADS box gene to a plant Y chromosome. Mol. Biol. Evol. 20: 1062-1069.
31. MILLS, R. E., C. T. LUTTIG, C. E. LARKINS, A. BEAUCHAMP, C. TSUI et al., 2006 An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16: 1182-1190.
32. MOESENEDER, M. M., J. M. ARRIETA, G. MUYZER, C. WINTER and G. J. HERNDL, 1999 Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525.
33. MOORE, R. C., O. KOZYREVA, S. LEBEL- HARDENACK, J. SIROKY, R. HOBZA et al., 2003 Genetic and functional analysis of DD44, a sex-linked gene from the dioecious plant Silene latifolia, provides clues to early events in sex chromosome evolution. Genetics 163: 321-334.
34. NAKAO, S., S. MATSUNAGA, A. SAKAI, T. KUROIWA and S. KAWANO, 2002 RAPD isolation of a Y chromosome specific ORF in a dioecious plant, Silene latifolia. Genome 45: 413-420.
35. NEGRUTIU, I., B. VYSKOT, N. BARBACAR, S. GEORGIEV and F. MONEGER, 2001 Dioecious plants. A key to the early events of sex chromosome evolution. Plant Physiol. 127: 1418-1424.
36. NICOLAS, M., G. MARAIS, V. HYKELOVA, B. JANOUSEK, V. LAPORTE et al., 2005 A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. PLoS Biol. 3: e4.
37. OBARA, M., S. MATSUNAGA, S. NAKAO and S. KAWANO, 2002 A plant Y chromosome-STS marker encoding a degenerate retrotransposon. Genes Genet. Syst. 77: 393-398.
38. OHTA, T., 1995 Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40: 56-63.
39. PALUMBI, S. R., and C. S. BAKER, 1994 Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol. Biol. Evol. 11: 426-435.
40. PEICHEL, C. L., J. A. ROSS, C. K. MATSON, M. DICKSON, J. GRIMWOOD et al., 2004 The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr. Biol. 14: 1416-1424.
41. PRITHAM, E. J., Y. H. ZHANG, C. FESCHOTTE and R. V. KESSELI, 2003 An Ac-like transposable element family with transcriptionally active Y-linked copies in the white campion, Silene latifolia. Genetics 165: 799-807.
42. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
43. SCHMIDT, W. M., and M. W. MUELLER, 1999 CapSelect: a highly sensitive method for 5′ CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs. Nucleic Acids Res. 27: e31.
44. SCHUELKE, M., 2000 An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233-234.
45. SCOTTI, I., and L. F. DELPH, 2006 Selective trade-offs and sex-chromosome evolution in Silene latifolia. Evolution Int. J. Org. Evolution 60: 1793-1800.
46. SHAKHNOVICH, B. E., and E. V. KOONIN, 2006 Origins and impact of constraints in evolution of gene families. Genome Res. 16: 1529-1536.
47. SKALETSKY, H., T. KURODA-KAWAGUCHI, P. J. MINX, H. S. CORDUM, L. HILLIER et al., 2003 The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837.
48. STREGE, M., and A. LAGU, 1991 Separation of DNA restriction fragments by capillary electrophoresis using coated fused silica capillaries. Anal. Chem. 63: 1233-1236.
49. SWERDLOW, H., and R. GESTELAND, 1990 Capillary gel electrophoresis for rapid, high resolution DNA sequencing. Nucleic Acids Res. 18: 1415-1419.
50. THOMAS, J. H., 2006 Concerted evolution of two novel protein families in Caenorhabditis species. Genetics 172: 2269-2281.
51. VALLENDER, E. J., and B. T. LAHN, 2004 How mammalian sex chromosomes acquired their peculiar gene content. BioEssays 26: 159-169.
52. VOS, P., R. HOGERS, M. BLEEKER, M. REIJANS, T. VAN DE LEE et al., 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 21: 4407-4414.
53. WALSH, J. B., 1995 How often do duplicated genes evolve new functions? Genetics 139: 421-428.
54. WOLFE, K. H., and D. C. SHIELDS, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
55. ZLUVOVA, J., B. JANOUSEK, I. NEGRUTIU and B. VYSKOT, 2005 Comparison of the X and Y chromosome organization in Silene latifolia. Genetics 170: 1431-1434.