A haploid system of sex determination in the brown alga ectocarpus sp.

Current Biology

Volumn 24, Issue 17, 2014, Pages 1945-1957

  Ahmed, Sophia ^a,b   Cock, J Mark ^a   Pessia, Eugenie ^c   Luthringer, Remy ^a   Cormier, Alexandre ^a   Robuchon, Marine ^a,h   Sterck, Lieven ^d   Peters, Akira F ^e   Dittami, Simon M ^a   Corre, Erwan ^g   Valero, Myriam ^h   Aury, Jean Marc ^f   Roze, Denis ^h   Van De Peer, Yves ^d,i   Bothwell, John ^b   Marais, Gabriel A B ^c   Coelho, Susana M ^a  

^a STATION BIOLOGIQUE DE ROSCOFF   (France)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c UNIVERSITÉ LYON 1   (France)

^d DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^e Bezhin Rosko   (France)

^f DIF   (France)

^g STATION BIOLOGIQUE   (France)

^h STATION BIOLOGIQUE DE ROSCOFF   (France)

ⁱ UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BROWN ALGA; GENETICS; GROWTH, DEVELOPMENT AND AGING; HAPLOIDY; SEX DETERMINATION PROCESS;

HAPLOIDY; PHAEOPHYTA; SEX DETERMINATION PROCESSES;

EID: 84907990399     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2014.07.042     Document Type: Article

References (75)

1. D. Charlesworth, B. Charlesworth, and G. Marais Steps in the evolution of heteromorphic sex chromosomes Heredity (Edinb) 95 2005 118 128
2. C.Y. Jordan, and D. Charlesworth The potential for sexually antagonistic polymorphism in different genome regions Evolution 66 2012 505 516
3. J.E. Ironside No amicable divorce? challenging the notion that sexual antagonism drives sex chromosome evolution Bioessays 32 2010 718 726
4. B.T. Lahn, and D.C. Page Four evolutionary strata on the human X chromosome Science 286 1999 964 967
5. H. Skaletsky, T. Kuroda-Kawaguchi, P.J. Minx, H.S. Cordum, L. Hillier, L.G. Brown, S. Repping, T. Pyntikova, J. Ali, and T. Bieri The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes Nature 423 2003 825 837
6. C. Lemaitre, M.D. Braga, C. Gautier, M.F. Sagot, E. Tannier, and G.A. Marais Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes Genome Biol. Evol. 1 2009 56 66
7. J. Wang, J.K. Na, Q. Yu, A.R. Gschwend, J. Han, F. Zeng, R. Aryal, R. VanBuren, J.E. Murray, and W. Zhang Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution Proc. Natl. Acad. Sci. USA 109 2012 13710 13715
8. J.J. Bull Evolution of Sex Determining Mechanisms 1983 Benjamin/ Cummings Menlo Park
9. J. Bull Sex chromosomes in haploid dioecy: a unique contrast to Muller's theory for diploid dioecy Am. Nat. 112 1978 245 250
10. D. Bachtrog, M. Kirkpatrick, J.E. Mank, S.F. McDaniel, J.C. Pires, W. Rice, and N. Valenzuela Are all sex chromosomes created equal? Trends Genet. 27 2011 350 357
11. D. Bachtrog Plant sex chromosomes: a non-degenerated Y? Curr. Biol. 21 2011 R685 R688
12. K.T. Yamato, K. Ishizaki, M. Fujisawa, S. Okada, S. Nakayama, M. Fujishita, H. Bando, K. Yodoya, K. Hayashi, and T. Bando Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system Proc. Natl. Acad. Sci. USA 104 2007 6472 6477
13. P. Ferris, B.J. Olson, P.L. De Hoff, S. Douglass, D. Casero, S. Prochnik, S. Geng, R. Rai, J. Grimwood, and J. Schmutz Evolution of an expanded sex-determining locus in Volvox Science 328 2010 351 354
14. S.F. McDaniel, K.M. Neubig, A.C. Payton, R.S. Quatrano, and D.J. Cove Recent gene-capture on the UV sex chromosome of the moss Ceratodon purpureus Evolution 67 2013 2811 2822
15. A.F. Peters, D. Marie, D. Scornet, B. Kloareg, and J.M. Cock Proposal of Ectocarpus siliculosus (Ectocarpales, Phaeophyceae) as a model organism for brown algal genetics and genomics J. Phycol. 40 2004 1079 1088
16. J.M. Cock, L. Sterck, P. Rouzé, D. Scornet, A.E. Allen, G. Amoutzias, V. Anthouard, F. Artiguenave, J.M. Aury, and J.H. Badger The Ectocarpus genome and the independent evolution of multicellularity in brown algae Nature 465 2010 617 621
17. S. Billiard, M. López-Villavicencio, B. Devier, M.E. Hood, C. Fairhead, and T. Giraud Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types Biol. Rev. Camb. Philos. Soc. 86 2011 421 442
18. M.E. Hood, E. Petit, and T. Giraud Extensive divergence between mating-type chromosomes of the anther-smut fungus Genetics 193 2013 309 315
19. A. Menkis, D.J. Jacobson, T. Gustafsson, and H. Johannesson The mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma represents a model for early evolution of sex chromosomes PLoS Genet. 4 2008 e1000030
20. G. Berthold Die geschlechtliche Fortpflanzung der eigentlichen Phaeosporeen Mitt. Zool. Stat. Neapel 2 1881 401 413
21. C. van den Hoek, D.G. Mann, and H.M. Jahns Algae: An Introduction to Phycology 1995 Cambridge University Press Cambridge
22. L.V. Evans A large chromosome in the laminarian nucleus Nature 198 1963 215
23. R.J. Lewis Chromosomes of the brown algae Phycologia 35 1996 19 40
24. D.G. Müller Sex expression in aneuploid gametophytes of the brown alga Ectocarpus siliculosus (Dillw.) Lyngb Arch. Protistenk. 117 1975 297 302
25. S.M. Dittami, C. Proux, S. Rousvoal, A.F. Peters, J.M. Cock, J.Y. Coppée, C. Boyen, and T. Tonon Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae) BMC Mol. Biol. 12 2011 2
26. S. Heesch, G.Y. Cho, A.F. Peters, G. Le Corguillé, C. Falentin, G. Boutet, S. Coëdel, C. Jubin, G. Samson, and E. Corre A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence New Phytol. 188 2010 42 51
27. A.B. Carvalho, and A.G. Clark Efficient identification of Y chromosome sequences in the human and Drosophila genomes Genome Res. 23 2013 1894 1907
28. P.M. Sharp, and W.H. Li The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications Nucleic Acids Res. 15 1987 1281 1295
29. D. Charif, J. Thioulouse, J.R. Lobry, and G. Perrière Online synonymous codon usage analyses with the ade4 and seqinR packages Bioinformatics 21 2005 545 547
30. S. Rozen, H. Skaletsky, J.D. Marszalek, P.J. Minx, H.S. Cordum, R.H. Waterston, R.K. Wilson, and D.C. Page Abundant gene conversion between arms of palindromes in human and ape Y chromosomes Nature 423 2003 873 876
31. C. Bartolomé, and B. Charlesworth Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes Genetics 174 2006 2033 2044
32. D. Bachtrog Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila Nat. Genet. 34 2003 215 219
33. E. Pessia, A. Popa, S. Mousset, C. Rezvoy, L. Duret, and G.A. Marais Evidence for widespread GC-biased gene conversion in eukaryotes Genome Biol. Evol. 4 2012 675 682
34. D. Bachtrog Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration Nat. Rev. Genet. 14 2013 113 124
35. W.G. Hill, and A. Robertson The effect of linkage on limits to artificial selection Genet. Res. 8 1966 269 294
36. B. Charlesworth, and D. Charlesworth The degeneration of Y chromosomes Philos. Trans. R. Soc. Lond. B Biol. Sci. 355 2000 1563 1572
37. D. Bachtrog The temporal dynamics of processes underlying Y chromosome degeneration Genetics 179 2008 1513 1525
38. A. Idnurm, F.J. Walton, A. Floyd, and J. Heitman Identification of the sex genes in an early diverged fungus Nature 451 2008 193 196
39. J.W. Foster, F.E. Brennan, G.K. Hampikian, P.N. Goodfellow, A.H. Sinclair, R. Lovell-Badge, L. Selwood, M.B. Renfree, D.W. Cooper, and J.A. Graves Evolution of sex determination and the Y chromosome: SRY-related sequences in marsupials Nature 359 1992 531 533
40. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Mol. Biol. Evol. 28 2011 2731 2739
41. F. Veyrunes, P.D. Waters, P. Miethke, W. Rens, D. McMillan, A.E. Alsop, F. Grützner, J.E. Deakin, C.M. Whittington, and K. Schatzkamer Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes Genome Res. 18 2008 965 973
42. L. Potrzebowski, N. Vinckenbosch, A.C. Marques, F. Chalmel, B. Jégou, and H. Kaessmann Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes PLoS Biol. 6 2008 e80
43. R. Bergero, and D. Charlesworth Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system Curr. Biol. 21 2011 1470 1474
44. J.D. Fry The genomic location of sexually antagonistic variation: some cautionary comments Evolution 64 2010 1510 1516
45. W.R. Rice Sex chromosomes and the evolution of sexual dimorphism Evolution 38 1984 735 742
46. H. Ellegren, and J. Parsch The evolution of sex-biased genes and sex-biased gene expression Nat. Rev. Genet. 8 2007 689 698
47. R. Assis, Q. Zhou, and D. Bachtrog Sex-biased transcriptome evolution in Drosophila Genome Biol. Evol. 4 2012 1189 1200
48. S.M. Coelho, O. Godfroy, A. Arun, G. Le Corguillé, A.F. Peters, and J.M. Cock OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus Proc. Natl. Acad. Sci. USA 108 2011 11518 11523
49. R. Bergero, and D. Charlesworth The evolution of restricted recombination in sex chromosomes Trends Ecol. Evol. 24 2009 94 102
50. H.S. Yoon, J.D. Hackett, C. Ciniglia, G. Pinto, and D. Bhattacharya A molecular timeline for the origin of photosynthetic eukaryotes Mol. Biol. Evol. 21 2004 809 818
51. M.V. Chibalina, and D.A. Filatov Plant Y chromosome degeneration is retarded by haploid purifying selection Curr. Biol. 21 2011 1475 1479
52. S. Qiu, R. Bergero, and D. Charlesworth Testing for the footprint of sexually antagonistic polymorphisms in the pseudoautosomal region of a plant sex chromosome pair Genetics 194 2013 663 672
53. H. Ellegren, and A. Carmichael Multiple and independent cessation of recombination between avian sex chromosomes Genetics 158 2001 325 331
54. M. Stöck, A. Horn, C. Grossen, D. Lindtke, R. Sermier, C. Betto-Colliard, C. Dufresnes, E. Bonjour, Z. Dumas, and E. Luquet Ever-young sex chromosomes in European tree frogs PLoS Biol. 9 2011 e1001062
55. B. Vicoso, V.B. Kaiser, and D. Bachtrog Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution Proc. Natl. Acad. Sci. USA 110 2013 6453 6458
56. C.E. Allen The genetics of bryophytes Bot. Rev. 1 1935 269 291
57. S.M. Coelho, D. Scornet, S. Rousvoal, N.T. Peters, L. Dartevelle, A.F. Peters, and J.M. Cock How to cultivate Ectocarpus Cold Spring Harb Protoc 2012 2012 258 261
58. M.G. Grabherr, B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, and Q. Zeng Full-length transcriptome assembly from RNA-Seq data without a reference genome Nat. Biotechnol. 29 2011 644 652
59. C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: discovering splice junctions with RNA-Seq Bioinformatics 25 2009 1105 1111
60. C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn, and L. Pachter Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat. Protoc. 7 2012 562 578
61. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
62. S. Anders, and W. Huber Differential expression analysis for sequence count data Genome Biol. 11 2010 R106
63. L. Sterck, K. Billiau, T. Abeel, P. Rouzé, and Y. Van de Peer ORCAE: online resource for community annotation of eukaryotes Nat. Methods 9 2012 1041
64. S. Foissac, J.P. Gouzy, S. Rombauts, C. Mathé, J. Amselem, L. Sterck, Y. Van de Peer, P. Rouzé, and T. Schiex Genome annotation in plants and fungi: EuGene as a model platform Current Bioinformatics 3 2008 87 97
65. S. Degroeve, Y. Saeys, B. De Baets, P. Rouzé, and Y. Van de Peer SpliceMachine: predicting splice sites from high-dimensional local context representations Bioinformatics 21 2005 1332 1338
66. T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville Considering transposable element diversification in de novo annotation approaches PLoS ONE 6 2011 e16526
67. C. Feschotte, U. Keswani, N. Ranganathan, M.L. Guibotsy, and D. Levine Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes Genome Biol. Evol. 1 2009 205 220
68. G.D. Schuler Sequence mapping by electronic PCR Genome Res. 7 1997 541 550
69. M. Gouy, S. Guindon, and O. Gascuel SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building Mol. Biol. Evol. 27 2010 221 224
70. J. Castresana Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 17 2000 540 552
71. Z. Yang PAML 4: phylogenetic analysis by maximum likelihood Mol. Biol. Evol. 24 2007 1586 1591
72. S. Penel, A.M. Arigon, J.F. Dufayard, A.S. Sertier, V. Daubin, L. Duret, M. Gouy, and G. Perrière Databases of homologous gene families for comparative genomics BMC Bioinformatics 10 Suppl 6 2009 S3
73. A. Löytynoja, and N. Goldman An algorithm for progressive multiple alignment of sequences with insertions Proc. Natl. Acad. Sci. USA 102 2005 10557 10562
74. T. Silberfeld, J.W. Leigh, H. Verbruggen, C. Cruaud, B. de Reviers, and F. Rousseau A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation" Mol. Phylogenet. Evol. 56 2010 659 674
75. J.W. Brown, and U. Sorhannus A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages PLoS ONE 5 2010 e12759