BACKGROUND: Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. RESULTS: Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30% of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. CONCLUSIONS: Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20%.

Department of Plant Developmental Genetics Institute of Biophysics of the CAS v v i Brno Czech Republic

Institute of Evolutionary Biology University of Edinburgh Edinburgh UK

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Holice Czech Republic

Institute of Integrative Biology ETH Zurich Zurich Switzerland

Laboratoire de Biométrie et Biologie Evolutive CNRS Université Lyon 1 Villeurbanne France

Pole Rhone Alpes de Bioinformatique Villeurbanne France

Unité de Recherche en Génomique Végétale INRA Université d'Evry Val d'Essonne ERL CNRS 8196 Evry France

Zobrazit více v PubMed

Bernasconi G, Antonovics J, Biere A, Charlesworth D, Delph LF, Filatov D, et al. Silene as a model system in ecology and evolution. Heredity. 2009;103(1):5–14. doi: 10.1038/hdy.2009.34. PubMed DOI

Ming R, Bendahmane A, Renner SS. Sex chromosomes in land plants. Annu Rev Plant Biol. 2011;62:485–514. doi: 10.1146/annurev-arplant-042110-103914. PubMed DOI

Filatov DA. Isolation of genes from plant Y chromosomes. Methods Enzymol. 2005;395:418–42. doi: 10.1016/S0076-6879(05)95023-4. PubMed DOI

Bergero R, Forrest A, Kamau E, Charlesworth D. Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: evidence from new sex-linked genes. Genetics. 2007;175(4):1945–54. doi: 10.1534/genetics.106.070110. PubMed DOI PMC

Bergero R, Qiu S, Forrest A, Borthwick H, Charlesworth D. Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes. Genetics. 2013;194(3):673–86. doi: 10.1534/genetics.113.150755. PubMed DOI PMC

Bergero R, Charlesworth D. Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system. Curr Biol. 2011;21(17):1470–4. doi: 10.1016/j.cub.2011.07.032. PubMed DOI

Chibalina MV, Filatov DA. Plant Y chromosome degeneration is retarded by haploid purifying selection. Curr Biol. 2011;21(17):1475–9. doi: 10.1016/j.cub.2011.07.045. PubMed DOI

Muyle A, Zemp N, Deschamps C, Mousset S, Widmer A, Marais G. Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes. PLoS Biol. 2012;10(4), e1001308. PubMed PMC

Sloan DB, Keller SR, Berardi AE, Sanderson BJ, Karpovich JF, Taylor DR. De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae) Mol Ecol Resour. 2012;12(2):333–43. doi: 10.1111/j.1755-0998.2011.03079.x. PubMed DOI

Ishii K, Amanai Y, Kazama Y, Ikeda M, Kamada H, Kawano S. Analysis of BAC clones containing homologous sequences on the end of the Xq arm and on chromosome 7 in the dioecious plant Silene latifolia. Genome. 2010;53(4):311–20. doi: 10.1139/G10-008. PubMed DOI

Blavet N, Blavet H, Cegan R, Zemp N, Zdanska J, Janousek B, et al. Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S. vulgaris autosome. BMC Genomics. 2012;13:226. doi: 10.1186/1471-2164-13-226. PubMed DOI PMC

Filatov DA. Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes. Genetics. 2005;170(2):975–9. doi: 10.1534/genetics.104.037069. PubMed DOI PMC

Bergero R, Charlesworth D, Filatov DA, Moore RC. Defining regions and rearrangements of the Silene latifolia Y chromosome. Genetics. 2008;178(4):2045–53. doi: 10.1534/genetics.107.084566. PubMed DOI PMC

Pritham EJ, Zhang YH, Feschotte C, Kesseli RV. An Ac-like transposable element family with transcriptionally active Y-linked copies in the white campion Silene latifolia. Genetics. 2003;165(2):799–807. PubMed PMC

Hobza R, Lengerova M, Svoboda J, Kubekova H, Kejnovsky E, Vyskot B. An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution. Chromosoma. 2006;115(5):376–82. doi: 10.1007/s00412-006-0065-5. PubMed DOI

Kejnovsky E, Kubat Z, Hobza R, Lengerova M, Sato S, Tabata S, et al. Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifolia. Genetica. 2006;128(1–3):167–75. doi: 10.1007/s10709-005-5701-0. PubMed DOI

Hobza R, Kejnovsky E, Vyskot B, Widmer A. The role of chromosomal rearrangements in the evolution of Silene latifolia sex chromosomes. Mol Genet Genomics. 2007;278(6):633–8. doi: 10.1007/s00438-007-0279-0. PubMed DOI

Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, Macas J, et al. Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes. Chromosome Res. 2008;16(7):961–76. doi: 10.1007/s10577-008-1254-2. PubMed DOI

Bergero R, Forrest A, Charlesworth D. Active miniature transposons from a plant genome and its non-recombining Y chromosome. Genetics. 2008;178(2):1085–92. PubMed PMC

Macas J, Kejnovsky E, Neumann P, Novak P, Koblizkova A, Vyskot B. Next generation sequencing-based analysis of repetitive DNA in the model dioecious plant Silene latifolia. PLoS ONE. 2011;6(11) doi: 10.1371/journal.pone.0027335. PubMed DOI PMC

Steflova P, Hobza R, Vyskot B, Kejnovsky E. Strong Accumulation of Chloroplast DNA in the Y Chromosomes of Rumex acetosa and Silene latifolia. Cytogenet Genome Res. 2013; 142(1):59-65. PubMed

Sykorova E, Cartagena J, Horakova M, Fukui K, Fajkus J. Characterization of telomere-subtelomere junctions in Silene latifolia. Mol Genet Genomics. 2003;269(1):13–20. PubMed

Scotti I, Delph LF. Selective trade-offs and sex-chromosome evolution in Silene latifolia. Evolution. 2006;60(9):1793–800. doi: 10.1111/j.0014-3820.2006.tb00523.x. PubMed DOI

Matsunaga S, Hizume M, Kawano S, Kuroiwa T. Cytological analysis in Melandrium album: genome size, chromosome size and fluorescence in situ hybridization. Cytologia. 1994;59:135–41. doi: 10.1508/cytologia.59.135. DOI

Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, et al. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014;508(7497):494–9. doi: 10.1038/nature13206. PubMed DOI PMC

Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, et al. Origins and functional evolution of Y chromosomes across mammals. Nature. 2014;508(7497):488–93. doi: 10.1038/nature13151. PubMed DOI

Guttman DS, Charlesworth D. An X-linked gene with a degenerate Y-linked homologue in a dioecious plant. Nature. 1998;393(6682):263–6. doi: 10.1038/30492. PubMed DOI

Kazama Y, Nishihara K, Bergero R, Fujiwara MT, Abe T, Charlesworth D, et al. SlWUS1; an X-linked gene having no homologous Y-linked copy in Silene latifolia. G3 (Bethesda) 2012;2(10):1269–78. doi: 10.1534/g3.112.003749. PubMed DOI PMC

Qiu S, Bergero R, Guirao-Rico S, Campos JL, Cezard T, Gharbi T, Charlesworth D. RAD-mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region. Molecular Ecology. 2015. in press. PubMed

Cegan R, Marais GA, Kubekova H, Blavet N, Widmer A, Vyskot B, et al. Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia. BMC Plant Biol. 2010;10:180. doi: 10.1186/1471-2229-10-180. PubMed DOI PMC

Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–5. doi: 10.1093/bioinformatics/btt086. PubMed DOI PMC

Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5(6) doi: 10.1371/journal.pone.0011147. PubMed DOI PMC

Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia

Dosage compensation evolution in plants: theories, controversies and mechanisms

Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

DNA methylation and genetic degeneration of the Y chromosome in the dioecious plant Silene latifolia

The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

Impact of repetitive DNA on sex chromosome evolution in plants

Zobrazit více v PubMed

GENBANK
KC977838, KC978922