Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes

Abstract

Background: The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific regions of the Y or the Yh chromosome (MSY or HSY). Therefore, repeat composition and distribution in the sex determining region of papaya sex chromosomes would be informative to understand how these repetitive sequences might be involved in the early stages of sex chromosome evolution.

Results: Detailed composition of interspersed, sex-specific, and tandem repeats was analyzed from 8.1 megabases (Mb) HSY and 5.3 Mb corresponding X chromosomal regions. Approximately 77% of the HSY and 64% of the corresponding X region were occupied by repetitive sequences. Ty3-gypsy retrotransposons were the most abundant interspersed repeats in both regions. Comparative analysis of repetitive sequences between the sex determining region of papaya X chromosome and orthologous autosomal sequences of Vasconcellea monoica, a close relative of papaya lacking sex chromosomes, revealed distinctive differences in the accumulation of Ty3-Gypsy, suggesting that the evolution of the papaya sex determining region may accompany Ty3-Gypsy element accumulation. In total, 21 sex-specific repeats were identified from the sex determining region; 20 from the HSY and one from the X. Interestingly, most HSY-specific repeats were detected in two regions where the HSY expansion occurred, suggesting that the HSY expansion may result in the accumulation of sex-specific repeats or that HSY-specific repeats might play an important role in the HSY expansion. The analysis of simple sequence repeats (SSRs) revealed that longer SSRs were less abundant in the papaya sex determining region than the other chromosomal regions.

Conclusion: Major repetitive elements were Ty3-gypsy retrotransposons in both the HSY and the corresponding X. Accumulation of Ty3-Gypsy retrotransposons in the sex determining region of papaya X chromosome was significantly higher than that in the corresponding region of V. monoica, suggesting that Ty3-Gypsy could be crucial for the expansion and evolution of the sex determining region in papaya. Most sex-specific repeats were located in the two HSY expansion regions.

Figure 1

Cumulative distributions of Ty3-gypsy and Ty1-copia long terminal repeat (LTR) elements in the sex-determining chromosome regions. (A) The cumulative increase of sequences occupied by Ty3-gypsy and Ty1-copia LTR elements in hermaphrodite-specific Y (HSY) chromosome region and its corresponding X region. (B) The cumulative numbers of Ty3-gypsy and Ty1-copia LTR elements in the HSY and the corresponding X region. The distance between two dots represents 250 kb. Colored bars at an X-axis denote regions with significantly low repeat contents in the HSY (red) or in the corresponding X region (blue).

Figure 2

Cumulative distributions of the sex-specific repeats identified from the sex-determining chromosome regions. (A) The accumulative number of each sex-specific repeat in the hermaphrodite-specific Y (HSY) chromosome region. (B) The accumulative number of each sex-specific repeat in the HSY-corresponding X region. In total, 21 sex-specific repeats were identified from the sex determining region; 20 from the HSY and one from the corresponding X. Most of HSY-specific repeats were located in two regions where the HSY expansion occurred.

Figure 3

Identification, validation, and phylogenetic analyses of sex-specific repeats in the sex determining chromosome regions. (A) Gel image of genomic PCR result from male-specificity test of HSY-R29 and HSY-R162 (SF: SunUp female, SH: SunUp hermaphrodite, AU9F: AU9 Female, AU9M: AU9 male). Phylogenetic analyses of papaya HSY-specific repeats, HSY-R162 (B) and HSY-R29 (C). Individual repeat ID represents its proximal location (bp) in the HSY.

Figure 4

Association of potential X-specific repeat in the exon duplication of papaya zinc finger protein. (A) Schematic demonstration of the duplication of X-specific repeat, X-R55, containing the 3rd exon of papaya zinc finger protein (accession ID: EX272522.1). (B) Phylogenetic tree of multiple X-R55 copies. The numbers at the root of each branch joining point are boot strap values. (C) Gel image of genomic PCR result for testing presence of the X-R55 (SF: SunUp female, SH: SunUp hermaphrodite, AU9F: AU9 Female, AU9M: AU9 male). (D) Gel image of RT-PCR result for testing the expression of papaya zinc finger protein in various tissues from SunUp and AU9 papaya (FF: female flower, FL: female leaf, HF: hermaphrodite flower, HL: hermaphrodite leaf, MF: male flower, ML: male leaf, SD: seeds, FT: 50% mature fruit). (E). Phylogenetic tree of papaya zinc finger protein (Cp zinc finger) with homologous proteins from other plant species with accession ID in NCBI.

Figure 5

Cumulative distributions of simple sequences repeats (SSRs) in the sex determining chromosome regions. SSRs with a length greater than 12 nucleotides, motif lengths of 2 to 6 bp, and a minimum of 5 repeats, were detected from the HSY and the corresponding X sequences. Number of total SSRs identified from each 0.5 Mb was plotted at the corresponding positions on the HSY and the corresponding X.