Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.

BIOGECO INRA University of Bordeaux 33610 Cestas France

Department of Biology Indiana University Bloomington IN 47405

Department of Ecology and Evolution University of Lausanne CH 1015 Switzerland

Department of Integrative Biology University of Texas Austin 78712 Texas

Department of Oncology John Radcliffe Hospital Oxford OX3 9DU United Kingdom

Department of Plant Developmental Genetics Institute of Biophysics Academy of Sciences of the Czech Republic 61200 Brno Czech Republic

Department of Plant Sciences University of Oxford OX1 3RB United Kingdom

Laboratoire Biométrie et Biologie Évolutive CNRS Université Lyon 1 69100 Villeurbanne France

University of Helsinki Institute of Biotechnology 00014 Finland

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Akagi T., Henry I. M., Tao R., Comai L., 2014.  A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons. Science 346: 646–650. 10.1126/science.1257225 PubMed DOI

Albritton S. E., Kranz A. L., Rao P., Kramer M., Dieterich C., et al. , 2014.  Sex-biased gene expression and evolution of the x chromosome in nematodes. Genetics 197: 865–883. 10.1534/genetics.114.163311 PubMed DOI PMC

Alexa A., Rahnenfuhrer J., 2010.  topGO: enrichment analysis for gene ontology. R package version 2: https://bioconductor.org/packages/release/bioc/html/topGO.html

Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J., 1990.  Basic local alignment search tool. J. Mol. Biol. 215: 403–410. 10.1016/S0022-2836(05)80360-2 PubMed DOI

Au K. F., Underwood J. G., Lee L., Wong W. H., 2012.  Improving PacBio long read accuracy by short read alignment. PLoS One 7: e46679 10.1371/journal.pone.0046679 PubMed DOI PMC

Baker D. A., Meadows L. A., Wang J., Dow J. A., Russell S., 2007.  Variable sexually dimorphic gene expression in laboratory strains of Drosophila melanogaster. BMC Genomics 8: 454 10.1186/1471-2164-8-454 PubMed DOI PMC

Benjamini Y., Hochberg Y., 1995.  Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289–300.

Benson G., 1999.  Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27: 573–580. 10.1093/nar/27.2.573 PubMed DOI PMC

Bergero R., Charlesworth D., 2009.  The evolution of restricted recombination in sex chromosomes. Trends Ecol. Evol. 24: 94–102. 10.1016/j.tree.2008.09.010 PubMed DOI

Bergero R., Forrest A., Kamau E., 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. 10.1534/genetics.106.070110 PubMed DOI PMC

Bergero R., Gardner J., Bader B., Yong L., Charlesworth D., 2019.  Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms. Proc. Natl. Acad. Sci. USA 116: 6924–6931. 10.1073/pnas.1818486116 PubMed DOI PMC

Blavet N., Blavet H., Muyle A., Käfer J., Cegan R., et al. , 2015.  Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics 16: 546 10.1186/s12864-015-1698-7 PubMed DOI PMC

Boetzer M., Henkel C. V., Jansen H. J., Butler D., Pirovano W., 2011.  Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578–579. 10.1093/bioinformatics/btq683 PubMed DOI

Bolger A. M., Lohse M., Usadel B., 2014.  Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Bray N. L., Pimentel H., Melsted P., Pachter L., 2016.  Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34: 525–527 (erratum: Nat. Biotechnol. 34: 888). 10.1038/nbt.3519 PubMed DOI

Broman K. W., Wu H., Sen S., Churchill G. A., 2003.  R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890. 10.1093/bioinformatics/btg112 PubMed DOI

Chan A. P., Crabtree J., Zhao Q., Lorenzi H., Orvis J., et al. , 2010.  Draft genome sequence of the oilseed species Ricinus communis. Nat. Biotechnol. 28: 951–956. 10.1038/nbt.1674 PubMed DOI PMC

Charlesworth B., 1991.  The evolution of sex chromosomes. Science 251: 1030–1033. 10.1126/science.1998119 PubMed DOI

Charlesworth B., Charlesworth D., 1978.  A model for the evolution of dioecy and gynodioecy. Am. Nat. 112: 975–997. 10.1086/283342 DOI

Charlesworth B., Charlesworth D., 2000.  The degeneration of Y chromosomes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355: 1563–1572. 10.1098/rstb.2000.0717 PubMed DOI PMC

Charlesworth D., 2015.  Plant contributions to our understanding of sex chromosome evolution. New Phytol. 208: 52–65. 10.1111/nph.13497 PubMed DOI

Charlesworth D., 2016.  Plant sex chromosomes. Annu. Rev. Plant Biol. 67: 397–420. 10.1146/annurev-arplant-043015-111911 PubMed DOI

Charlesworth D., Charlesworth B., Marais G. A., 2005.  Steps in the evolution of heteromorphic sex chromosomes. Heredity 95: 118–128. 10.1038/sj.hdy.6800697 PubMed DOI

Conesa A., Gotz S., Garcia-Gomez J. M., Terol J., Talon M., et al. , 2005.  Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674–3676. PubMed

Connallon T., Clark A. G., 2010.  Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression. Evolution 64: 3417–3442. 10.1111/j.1558-5646.2010.01136.x PubMed DOI PMC

Dag O., Asar O., Ilk O., 2014.  A methodology to implement Box-Cox transformation when no covariate is available. Commun. Stat. Simul. Comput. 43: 1740–1759. 10.1080/03610918.2012.744042 DOI

Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., et al. , 2011.  The variant call format and VCFtools. Bioinformatics 27: 2156–2158. 10.1093/bioinformatics/btr330 PubMed DOI PMC

Dawson T. E., Geber M. A., 1999.  Sexual dimorphism in physiology and morphology, pp. 175–215 in Gender and Sexual Dimorphism in Flowering Plants, edited by Geber M. A., Dawson T. E., Delph L. F. Springer, Heidelberg, Germany: 10.1007/978-3-662-03908-3_7 DOI

Delph D. F., 1999.  Sexual dimorphism in life history, pp. 149–173 in Gender and Sexual Dimorphism in Flowering Plants, edited by Geber M. A., Dawson T. E., Delph L. F. Springer, Heidelberg, Germany: 10.1007/978-3-662-03908-3_6 DOI

Delph L. F., Arntz A. M., Scotti-Saintagne C., Scotti I., 2010.  The genomic architecture of sexual dimorphism in the dioecious plant Silene latifolia. Evolution 64: 2873–2886. PubMed

DePristo M. A., Banks E., Poplin R., Garimella K. V., Maguire J. R., et al. , 2011.  A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491–498. 10.1038/ng.806 PubMed DOI PMC

Durand B., 1963.  Le complèxe Mercurialis annua L. s.l.: Une étude biosystématique. Annales des Sciences Naturelles, Botanique, Paris 12: 579–736.

Durand B., Durand R., 1991.  Sex determination and reproductive organ differentiation in Mercurialis. Plant Sci. 80: 49–65. 10.1016/0168-9452(91)90272-A DOI

Durand B., Louis J. P., Hamdi S., Cabre E., Yu L. X., et al. , 1987.  Major regulator genes, phytohormone levels and specific gene-expression for reproductive organogenesis in Mercurialis annua L. (2n=16). J. Cell. Biochem. 1987: 18–20.

Eckhart V. M., 1999.  Sexual dimorphism in flowers and inflorescences, pp. 123–148 in Gender and Sexual Dimorphism in Flowering Plants, edited by Geber M. A., Dawson T. E., Delph L. F. Springer, Heidelberg, Germany: 10.1007/978-3-662-03908-3_5 DOI

English A. C., Richards S., Han Y., Wang M., Vee V., et al. , 2012.  Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7: e47768 10.1371/journal.pone.0047768 PubMed DOI PMC

Fechter I., Hausmann L., Daum M., Sörensen T. R., Viehöver P., et al. , 2012.  Candidate genes within a 143 kb region of the flower sex locus in Vitis. Mol. Genet. Genomics 287: 247–259. 10.1007/s00438-012-0674-z PubMed DOI

Geraldes A., Hefer C. A., Capron A., Kolosova N., Martinez-Nuñez F., et al. , 2015.  Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol. Ecol. 24: 3243–3256. 10.1111/mec.13126 PubMed DOI

Gibson J. R., Chippindale A. K., Rice A. M., 2002.  The X chromosome is a hot spot for sexually antagonistic fitness variation. Proc. Biol. Sci. 269: 499–505. 10.1098/rspb.2001.1863 PubMed DOI PMC

González-Martínez S. C., Ridout K., Pannell J. R., 2017.  Range expansion compromises adaptive evolution in an outcrossing plant. Curr. Biol. 27: 2544–2551.e4. 10.1016/j.cub.2017.07.007 PubMed DOI

Haas B. J., Papanicolaou A., Yassour M., Grabherr M., Blood P. D., et al. , 2013.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8: 1494–1512. 10.1038/nprot.2013.084 PubMed DOI PMC

Harris, R. S., 2007 Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University, State College, PA.

Hesse E., Pannell J., 2011.  Sexual dimorphism in a dioecious population of the wind-pollinated herb Mercurialis annua: the interactive effects of resource availability and competition. Ann. Bot. 107: 1039–1045. 10.1093/aob/mcr046 PubMed DOI PMC

Hill W. G., Robertson A., 1966.  The effect of linkage on limits to artificial selection. Genet. Res. 8: 269–294. 10.1017/S0016672300010156 PubMed DOI

Hobza R., Cegan R., Jesionek W., Kejnovsky E., Vyskot B., et al. , 2017.  Impact of repetitive elements on the Y chromosome formation in plants. Genes (Basel) 8: E302 10.3390/genes8110302 PubMed DOI PMC

Horovitz S., Jiménez H., 1967.  Cruzamientos interespecíficos e intergenéricos en Caricaceas y sus implicaciones fitotécnicas. Agron. Trop. 17: 323–343.

Hough J., Hollister J. D., Wang W., Barret S. C. H., Wright S. I., 2014.  Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. Proc. Natl. Acad. Sci. USA 111: 7713–7718. 10.1073/pnas.1319227111 PubMed DOI PMC

Huang X., Madan A., 1999.  CAP3: a DNA sequence assembly program. Genome Res. 9: 868–877. 10.1101/gr.9.9.868 PubMed DOI PMC

Hunt M., Kikuchi T., Sanders M., Newbold C., Berriman M., et al. , 2013.  REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14: R47 10.1186/gb-2013-14-5-r47 PubMed DOI PMC

Katoh K., Standley D. M., 2013.  MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772–780. 10.1093/molbev/mst010 PubMed DOI PMC

Kazama Y., Ishii K., Aonuma W., Ikeda T., Kawamoto H., et al. , 2016.  A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome. Sci. Rep. 6: 18917 10.1038/srep18917 PubMed DOI PMC

Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., et al. , 2012.  Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. 10.1093/bioinformatics/bts199 PubMed DOI PMC

Khadka D. K., Nejidat A., Tal M., Golan-Goldhirsh A., 2002.  DNA markers for sex: molecular evidence for gender dimorphism in dioecious Mercurialis annua L. Mol. Breed. 9: 251–257. 10.1023/A:1020361424758 DOI

Khadka D. K., Nejidat A., Tal M., Golan-Goldhirsh A., 2005.  Molecular characterization of a gender-linked DNA marker and a related gene in Mercurialis annua L. Planta 222: 1063–1070. 10.1007/s00425-005-0046-6 PubMed DOI

Koboldt D. C., Chen K., Wylie T., Larson D. E., McLellan M. D., et al. , 2009.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283–2285. 10.1093/bioinformatics/btp373 PubMed DOI PMC

Krähenbühl M., Yuan Y. M., Küpfer P., 2002.  Chromosome and breeding system evolution of the genus Mercurialis (Euphorbiaceae): implications of ITS molecular phylogeny. Plant Syst. Evol. 234: 155–169. 10.1007/s00606-002-0208-y DOI

Krasovec M., Chester M., Ridout K., Filatov D. A., 2018.  The mutation rate and the age of the sex chromosomes in Silene latifolia. Curr. Biol. 28: 1832–1838.e4. 10.1016/j.cub.2018.04.069 PubMed DOI

Kuhn E., 1939.  Selbstbestäubungen subdiöcischer Blütenpflanzen, ein neuer Beweis für die genetische Theorie der Geschlechtsbestimmung. Planta 30: 457–470. 10.1007/BF01917065 DOI

Labouche A. M., Pannell J. R., 2016.  A test of the size-constraint hypothesis for a limit to sexual dimorphism in plants. Oecologia 181: 873–884. 10.1007/s00442-016-3616-3 PubMed DOI

Lahn B. T., Page D. C., 1999.  Four evolutionary strata on the human X chromosome. Science 286: 964–967 (erratum: Science 286: 2273). 10.1126/science.286.5441.964 PubMed DOI

Langmead B., Salzberg S. L., 2012.  Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357–359. 10.1038/nmeth.1923 PubMed DOI PMC

Leder E. H., Cano J. M., Leinonen T., O’Hara R. B., Nikinmaa M., et al. , 2010.  Female-biased expression on the X chromosome as a key step in sex chromosome evolution in threespine sticklebacks. Mol. Biol. Evol. 27: 1495–1503. 10.1093/molbev/msq031 PubMed DOI

Li H., Durbin R., 2009.  Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., et al. , 2009.  The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Li X., Veltsos P., Cossard G., Gerchen J., Pannell J.R., 2019 YY males of the dioecious plant Mercurialis annua are fully viable but produce largely infertile pollen. New Phytol. (in press). 10.1101/658708 PubMed DOI PMC

Liu Z., Moore P. H., Ma H., Ackerman C. M., Raglba M., et al. , 2004.  A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348–352. 10.1038/nature02228 PubMed DOI

Loeptien H., 1979.  Identification of the sex chromosome pair in asparagus (Asparagus officinalis L.). Zeitschrift fur Pflanzenzüchtung 82: 162–173.

Lüdecke, D., 2017 sjPlot: data visualization for statistics in social science. R package version 2.4.0. Accessed November 2018. Available at: https://CRAN.R-project.org/package=sjPlot.

Luo R., Liu B., Xie Y., Li Z., Huang W., et al. , 2012.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1: 18 [corrigenda: Gigascience 4: 30 (2015)]. 10.1186/2047-217X-1-18 PubMed DOI PMC

Mank J. E., 2013.  Sex chromosome dosage compensation: definitely not for everyone. Trends Genet. 29: 677–683. 10.1016/j.tig.2013.07.005 PubMed DOI

Mank J. E., Ellegren H., 2009.  Are sex-biased genes more dispensable. Biol. Lett. 5: 409–412. 10.1098/rsbl.2008.0732 PubMed DOI PMC

Marçais G., Kingsford C., 2011.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27: 764–770. 10.1093/bioinformatics/btr011 PubMed DOI PMC

McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., et al. , 2010.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297–1303. 10.1101/gr.107524.110 PubMed DOI PMC

Meisel R. P., Malone J. H., Clark A. G., 2012.  Disentangling the relationship between sex-biased gene expression and X-linkage. Genome Res. 22: 1255–1265. 10.1101/gr.132100.111 PubMed DOI PMC

Mohanty J. N., Nayak S., Jha S., Joshi R. K., 2017.  Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.). Voigt. Gene 626: 395–406. 10.1016/j.gene.2017.05.058 PubMed DOI

Montgomery S. H., Mank J. E., 2016.  Inferring regulatory change from gene expression: the confounding effects of tissue scaling. Mol. Ecol. 25: 5114–5128. 10.1111/mec.13824 PubMed DOI

Morgulis A., Gertz E. M., Schäffer A. A., Agarwala R., 2006.  A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13: 1028–1040. 10.1089/cmb.2006.13.1028 PubMed DOI

Muyle A., Käfer J., Zemp N., Mousset S., Picard F., et al. , 2016.  SEX-DETector: a probabilistic approach to study sex chromosomes in non-model organisms. Genome Biol. Evol. 8: 2530–2543. 10.1093/gbe/evw172 PubMed DOI PMC

Nam K., Ellegren H., 2008.  The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics 180: 1131–1136. 10.1534/genetics.108.090324 PubMed DOI PMC

Nielsen R., Yang Z., 1998.  Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929–936. PubMed PMC

Obbard D. J., Harris S. A., Buggs R. J. A., Pannell J., 2006.  Hybridization, polyploidy, and the evolution of sexual systems in Mercurialis (Euphorbiaceae). Evolution 60: 1801–1815. 10.1111/j.0014-3820.2006.tb00524.x PubMed DOI

Ono T., 1939.  Polyploidy and sex determination in Melandrium. I. Colcicine-induced polyploids of Melandrium album. Botanical Magazine 53: 549–556. 10.15281/jplantres1887.53.549 DOI

Ossowski S., Schneeberger K., Lucas-Lledó J. I., Warthmann N., Clark R. M., et al. , 2010.  The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92–94. 10.1126/science.1180677 PubMed DOI PMC

Pannell J., Dorken M. E., Pujol B., Berjano R., 2008.  Gender variation and transitions between sexual systems in Mercurialis annua (Euphorbiaceae). Int. J. Plant Sci. 169: 129–139. 10.1086/523360 DOI

Paolucci I., Gaudet M., Jorge V., Beritognolo I., Terzoli S., et al. , 2010.  Genetic linkage maps of Populus alba L. and comparative mapping analysis of sex determination across Populus species. Tree Genetics &amp. Genomes 6: 863–875.

Papadopulos A. S., Chester M., Ridout K., Filatov D. A., 2015.  Rapid Y degeneration and dosage compensation in plant sex chromosomes. Proc. Natl. Acad. Sci. USA 112: 13021–13026. 10.1073/pnas.1508454112 PubMed DOI PMC

Parisi M., Nuttall R., Naiman D., Bouffard G., Malley J., et al. , 2003.  Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299: 697–700. 10.1126/science.1079190 PubMed DOI PMC

Parsch J., Ellegren H., 2013.  The evolutionary causes and consequences of sex-biased gene expression. Nat. Rev. Genet. 14: 83–87. 10.1038/nrg3376 PubMed DOI

Picq S., Santoni S., Lacombe T., Latreille M., Weber A., et al. , 2014.  A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC Plant Biol. 14: 229 10.1186/s12870-014-0229-z PubMed DOI PMC

Pucholt P., Rönnberg-Wästljung A. C., Berlin S., 2015.  Single locus sex determination and female heterogamety in the basket willow (Salix viminalis l.). Heredity 114: 575–583. 10.1038/hdy.2014.125 PubMed DOI PMC

Pucholt P., Wright A. E., Liu Conze L., Mank J. E., Berlin S., 2017.  Recent sex chromosome divergence despite ancient dioecy in the willow Salix viminalis. Mol. Biol. Evol. 34: 1991–2001. 10.1093/molbev/msx144 PubMed DOI PMC

Puterova J., Kubat Z., Kejnovsky E., Jesionek W., Cizkova J., et al. , 2018.  The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons. BMC Genomics 19: 153 10.1186/s12864-018-4547-7 PubMed DOI PMC

Qiu S., Bergero R., Forrest A., Kaiser V. B., Charlesworth D., 2010.  Nucleotide diversity in Silene latifolia autosomal and sex-linked genes. Proc. Biol. Sci. 277: 3283–3290. 10.1098/rspb.2010.0606 PubMed DOI PMC

Quandt H. J., Pühler A., Broer I., 1993.  Transgenic root nodules of Vicia hirsuta: a fast and efficient system for the study of gene expression in indeterminate-type nodules. Mol. Plant Microbe Interact. 6: 699–706. 10.1094/MPMI-6-699 DOI

Rahman A. Y., Usharraj A. O., Misra B. B., Thottathil G. P., Jayasekaran K., et al. , 2013.  Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics 14: 75 10.1186/1471-2164-14-75 PubMed DOI PMC

Rastas P., 2017.  Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33: 3726–3732. 10.1093/bioinformatics/btx494 PubMed DOI

Rautenberg A., Filatov D., Svennblad B., Heidari N., Oxelman B., 2008.  Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene. BMC Evol. Biol. 8: 299 10.1186/1471-2148-8-299 PubMed DOI PMC

R Development Core Team, 2007 R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing. Vienna. ISBN 3–900051–07–0, Available at: http://www.R-project.org.

Renner S. S., 2014.  The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database. Am. J. Bot. 101: 1588–1596. 10.3732/ajb.1400196 PubMed DOI

Rice W. R., 1987.  The accumulation of sexually antagonistic genes as a selective agent promoting the evolution of reduced recombination between primitive sex chromosomes. Evolution 41: 911–914. 10.1111/j.1558-5646.1987.tb05864.x PubMed DOI

Robinson M. D., McCarthy D. J., Smyth G. K., 2010.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140. 10.1093/bioinformatics/btp616 PubMed DOI PMC

Russell J. R. W., Pannell J., 2015.  Sex determination in dioecious Mercurialis annua and its close diploid and polyploid relatives. Heredity 114: 262–271. 10.1038/hdy.2014.95 PubMed DOI PMC

Sanderson B. J., Wang L., Tiffin P., Wu Z., Olson M. S., 2018.  Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera. New Phytol. 221: 527–539. PubMed

Sato S., Hirakawa H., Isobe S., Fukai E., Watanabe A., et al. , 2011.  Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res. 18: 65–76. 10.1093/dnares/dsq030 PubMed DOI PMC

Schmieder R., Edwards R., 2011.  Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863–864. 10.1093/bioinformatics/btr026 PubMed DOI PMC

Sharma E., Künstner A., Fraser B. A., Zipprich G., Kottler V. A., et al. , 2014.  Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genomics 15: 400 10.1186/1471-2164-15-400 PubMed DOI PMC

Simão F. A., Waterhouse R. M., Ioannidis P., Kriventseva E. V., Zdobnov E. M., 2015.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210–3212. 10.1093/bioinformatics/btv351 PubMed DOI

Smarda P., Bureš P., Smerda J., Horová L., 2012.  Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability. New Phytol. 193: 513–521. 10.1111/j.1469-8137.2011.03942.x PubMed DOI

Smit, A. F. A., R. Hubley, and P. Green, 2013 RepeatMasker Open-4.0. Accessed February 2019. Available at: http://www.repeatmasker.org.

Smith B., 1955.  Sex chromosomes and natural polyploidy in dioecious Rumex. J. Hered. 46: 226–232. 10.1093/oxfordjournals.jhered.a106563 DOI

Smith S. A., Donoghue M. J., 2008.  Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86–89. 10.1126/science.1163197 PubMed DOI

Stamatakis A., 2014.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. 10.1093/bioinformatics/btu033 PubMed DOI PMC

Telgmann-Rauber A., Jamsari A., Kinney M. S., Pires J. C., Jung C., 2007.  Genetic and physical maps around the sex-determining M-locus of the dioecious plant Asparagus. Mol. Genet. Genomics 278: 221–234. 10.1007/s00438-007-0235-z PubMed DOI

Tennessen J. A., Govindarajulu R., Liston A., Ashman T. L., 2016.  Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex‐determining region. New Phytol. 211: 1412–1423. 10.1111/nph.13983 PubMed DOI PMC

Toups M., Rodrigues N., Perrin N., Kirkpatrick M., 2019.  A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Mol. Ecol. 28: 1877–1889. 10.1111/mec.14990 PubMed DOI PMC

Trombetta B., Sellitto D., Scozzari R., Cruciani F., 2014.  Inter- and intraspecies phylogenetic analyses reveal ex-tensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes. Mol. Biol. Evol. 31: 2108–2123. 10.1093/molbev/msu155 PubMed DOI PMC

Tsagkogeorga G., Cahais V., Galtier N., 2012.  The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis. Genome Biol. Evol. 4: 740–749. 10.1093/gbe/evs054 PubMed DOI PMC

Veltsos P., Cossard G., Beaudoing E., Beydon G., Savova Bianchi D., et al. , 2018.  Size and content of the sex-determining region of the Y chromosome in dioecious Mercurialis annua, a plant with homomorphic sex chromosomes. Genes (Basel) 9: E277 10.3390/genes9060277 PubMed DOI PMC

Vurture G. W., Sedlazeck F. J., Nattestad M., Underwood C. J., Fang H., et al. , 2017.  GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33: 2202–2204. 10.1093/bioinformatics/btx153 PubMed DOI PMC

Wang J., Na J. K., Yu Q., Gschwend A. R., Han J., et al. , 2012.  Sequencing papaya X and Y-h chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc. Natl. Acad. Sci. USA 109: 13710–13715. 10.1073/pnas.1207833109 PubMed DOI PMC

Wang K., Wang Z., Li F., Ye W., Wang J., et al. , 2012.  The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44: 1098–1103. 10.1038/ng.2371 PubMed DOI

Westergaard M., 1958.  The mechanism of sex determination in dioecious splants. Adv. Genet. 9: 217–281. 10.1016/S0065-2660(08)60163-7 PubMed DOI

Wright A. E., Darolti I., Bloch N. I., Oostra V., Sandkam B., et al. , 2017.  Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nat. Commun. 8: 14251 10.1038/ncomms14251 PubMed DOI PMC

Wu C. I., Davis A. W., 1993.  Evolution of postmating reproductive isolation: the composite nature of Haldane’s rule and its genetic bases. Am. Nat. 142: 187–212. 10.1086/285534 PubMed DOI

Wu M., Moore R. C., 2015.  The evolutionary tempo of sex chromosome degradation in Carica papaya. J. Mol. Evol. 80: 265–277. 10.1007/s00239-015-9680-1 PubMed DOI

Wu T. D., Watanabe C. K., 2005.  GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859–1875. 10.1093/bioinformatics/bti310 PubMed DOI

Wu X., Wang J., Na J. K., Yu Q., Moore R. C., et al. , 2010.  The origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea. Plant J. 63: 801–810. 10.1111/j.1365-313X.2010.04284.x PubMed DOI

Xue W., Li J. T., Zhu Y. P., Hou G. Y., Kong X. F., et al. , 2013.  L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14: 604 10.1186/1471-2164-14-604 PubMed DOI PMC

Yamamoto K., Oda Y., Haseda A., Fujito S., Mikami T., et al. , 2014.  Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region. Heredity 112: 317–324. 10.1038/hdy.2013.112 PubMed DOI PMC

Yang Z., 2007.  PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586–1591. 10.1093/molbev/msm088 PubMed DOI

Zemp N., Tavares R., Muyle A., Charlesworth D., Marais G. A., et al. , 2016.  Evolution of sex-biased gene expression in a dioecious plant. Nat. Plants 2: 16168 10.1038/nplants.2016.168 PubMed DOI

Li X., Veltsos P., Cossard G., Gerchen J., Pannell J. R., 2019.  YY males of the dioecious plant Mercurialis annua are fully viable but produce largely infertile pollen. New Phytol. (in press). .org/10.1101/658708 PubMed PMC

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