Construction of physical maps for the sex-specific regions of papaya sex chromosomes

Abstract

BackgroundPapaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male), XYh (hermaphrodite), and XX (female). The papaya hermaphrodite-specific Yh chromosome region (HSY) is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement.ResultsA reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC) libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89%) DNA sequence expansion.ConclusionThe 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2–3 million years ago. The genetically defined borders coincide with the common BACs on the minimum tiling paths of HSY and X. The minimum tiling paths of HSY and its X counterpart are being used for sequencing these X and Yh-specific regions.

Sequencing papaya X and Y h chromosomes reveals molecular basis of incipient sex chromosome evolution

“…1), which is indeed present on both the X and Y h chromosomes at the same location (36). In the HSY physical map, but not that of the X, there is a gap between border A and Knob 2; Knob 1 could not be mapped in the HSY due to high sequence similarity with Knob 1 in the X (35).…”

“…S2B). The molecular HSY border B, where sequence homology with the X region becomes high, lies about 277 kb beyond the genetically defined border; this 277-kb region makes up about 50% of the collinear region and is still recombining, as seen by the fine mapping carried out by Na et al (35).…”

“…The physical map of the X region corresponding to the HSY region consists of 43 BACs in a minimum tiling path with one gap in the middle, which is contiguous in the HSY physical map (35). Sequencing the highly repetitive HSY and its X counterpart is challenging even using a BAC-by-BAC approach.…”

Rapid divergence and expansion of the X chromosome in papaya

“…FISH analyses previously mapped the centromere of the Y h chromosome near Knob 4 (27); the X chromosome sequence does not have this knob, but a gap in the X physical map remains, because of repetitive sequences, in a location homologous to sequences close to Knobs 3 and 5 (SI Appendix, Fig. S4A) (3,27).…”

“…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)(2)(3). Papaya has two slightly different Y chromosomes that diverged about 73,000 y ago, Y in males and Y h in hermaphrodites (4).…”