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

Abstract

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.

Fig. 1.

Comparison between the arrangement of 70 genes on the HSY with homologous copies on the X (HSY-X gene pairs, see text). Each gene’s location is indicated by a horizontal line. The vertical black lines indicate the HSY and X sequences, and the sequences encoding the transcripts are numbered according to their order in the X region. The solid yellow circles indicate four heterochromatic knobs (Knobs 2–5) in the HSY (30) and Knob 1 in the X. Knobs 2–5 are specific to the HSY, but their estimated corresponding positions in the X region are indicated by empty yellow circles. Green labels indicate that both transcript copies are functional genes, blue labels indicate that the HSY transcript is a pseudogene, red labels indicate that the X transcript is a pseudogene, and purple labels indicate that both HSY and X copies are pseudogenes. The two inverted regions and the collinear region are marked. Inversion 1 in the HSY was split into two regions due to translocation.

Fig. 2.

Plot of synonymous site divergence (K_s) of 70 paired X/HSY genes arranged according to the location on the X chromosome. Horizontal lines indicate the mean K_s value of the genes found in each region (inversion 1, inversion 2, and collinear). Divergence values are significantly different between inversion 1, inverion 2, and the collinear region (P < 0.01). Gene pair names for each stratum are given in SI Appendix, Table S6.