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Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y h ).To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y h chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y h chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.Carica papaya | DNA sequencing | molecular evolution | sex chromosomes S ex chromosomes have evolved independently in diverse lineages of animals and plants, and new dioecious species are still evolving (1, 2). Evidence of homology between nascent sex chromosome pairs in flowering plants and fish (3-6) supports the notion that sex chromosomes evolved from autosomes that gained sex determination genes. The key event in sex chromosome evolution is the suppression of recombination between the sex-determining regions of ancestrally homologous chromosome pairs, which limits one chromosome of the pair to one sex, producing XY (male heterogametic) or ZW (female heterogametic) systems. Evolutionary models predict that a lack of recombination allows for Y-or W-specific characteristics to accumulate, through the reduced efficacy of selection on these chromosomes (7,8), leading to the Y and W chromosomes accumulating deleterious mutations and transposable elements, and ultimately undergoing genetic degeneration, through the loss of genes or gene functions, as observed in mammals, Drosophila, birds, fishes, and snakes (9, 10). In some animals and plants, the greater number of mitotic cell divisions in spermatogenesis than oogenesis also leads to Y chromosomes having a higher mutation rate than autosomes or X chromosomes (11)(12)(13)(14) and is predicted to further contribute to greater changes of the evolving Y (or W) chromosome than the X (or Z) chromosome.To test these predictions of repetitive sequence accumulation, chromosoma...

BackgroundPapaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly.ResultsThe physical map consists of 963 contigs, representing 9.4× genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes.ConclusionA BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics and map-based cloning of agronomically and economically important genes and for sex chromosome research.

Sex of dioecious and gynodioecious papayas is controlled by two slightly different Y chromosomes, Y for males and Y h for hermaphrodites. All combinations of the Y and/or Y h chromosomes are lethal. We investigated the features of paired dioecious X-and Y-specific bacterial artificial chromosomes (BACs) and compared their sequences to corresponding gynodioecious X-and Y-specific BACs. Numerous chromosomal rearrangements were detected between the X-and Y-specific BACs, including inversions, deletions, insertions, and duplications. DNA sequence expansion was documented on the Y BAC. Dioecious and gynodioecious X-specific BACs were virtually identical. The Y-and Y h -specific BACs shared high degree of DNA sequence identity, but local chromosomal rearrangements were detected, as the consequence of suppression of recombination in the male specific region and the isolation of Y and Y h chromosomes enforced by the lethal effect. Analysis of sequence divergence between three dioecious X and Y gene pairs resulted in the estimated ages of divergence from 0.6 to 2.5 million years, reinforcing the hypothesis of a recent origin of the papaya sex chromosomes. The estimated age of divergence between Y and Y h chromosomes was approximately 73,000 years for Gene 5. Our findings indicate that Y and Y h chromosomes evolved from a common ancestral Y chromosome, possibly prior to the origin of agriculture. The existence of a hermaphrodite Y h chromosome is less likely to have resulted from human selection as once suggested.

X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious Vasconcellea monoica, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12 V. monoica bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined V. monoica X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the V. monoica genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcriptencoding sequences, only 6 of which are functional X/V. monoica gene pairs. Sequence divergence from the V. monoica orthologs is almost identical for papaya X and Y alleles; the Carica-Vasconcellea split therefore occurred before the papaya sex chromosomes stopped recombining, making V. monoica a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Y h chromosome and V. monoica have all gained and lost genes, including a surprising amount of changes in the X.Carica papaya | gene gains and losses | sex chromosome evolution | suppression of recombination | centromere of X chromosome P apaya (Carica papaya L.) is a trioecious tropical fruit crop that has a nascent XY sex chromosome system, in which the sex determining region occupies a small fraction of the X/Y chromosome pair (1-3). Papaya has two slightly different Y chromosomes that diverged about 73,000 y ago, Y in males and Y h in hermaphrodites (4). All genotypes without X chromosomes (YY, YY h , and Y h Y h ) are lethal in early development, resulting in 25% aborted seeds in selfed hermaphrodites and in crosses between hermaphrodites and males (5), indicating that both Y types have lost at least one gene essential for development.Papaya belongs to the family Caricaceae, with six genera and 35 species, 32 of which are dioecious, two are trioecious (with male, female, and hermaphrodite individuals) and one, Vasconcellea monoica, is monoecious (with male and female flowers on a single plant). The predominance of dioecious species suggests that dioecy is ancestral in this family and that the trioecious and monoecious species evolved recently. V. monoica has no sex chromosomes, because there is no sexual dimorphism among individuals, and there is a single sequence corresponding to each of the several papaya X/Y h gene pairs tested, whereas distinct X and Y alleles were detected in several dioecious Vasconcellea species (6), which indicates that the sex chromosomes in these species are homologous with those in papaya.V. monoica therefore provides an opportunity to compare the recentl...