Abstract

BackgroundThe 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.ResultsDetailed 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.ConclusionMajor 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-335) contains supplementary material, which is available to authorized users.

Highlights

  • 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

  • Long terminal repeats (LTRs) accounted for more than 97% of all identifiable retroelements in all three sources of sequences and the Ty3-gypsy element was the most abundant LTR in the Hermaphrodite-specific region of the Y chromosome (HSY) and the corresponding X, whereas Ty1-copia element was more abundant in V. monoica (Table 1)

  • To examine the portion of papaya-specific repeats accounting for interspersed repeats, the HSY and the corresponding X sequences were masked by only known repeats, consisting of Repbase and TIGR repeats excluding papaya repeats

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Summary

Introduction

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). 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. The Caricaceae family consists of 35 species; one monoecious, 32 dioecious, and two trioecious species, providing an invaluable system for studying plant sex determination. Papaya is a trioecious species with three sex phenotypes; female, male, and hermaphrodite. Female papaya has homogametic XX chromosomes, whereas male and hermaphrodite plants have heterogametic XY chromosomes. The male and the hermaphrodite have slightly different Y chromosomes, Y for males and Yh for hermaphrodites [3,4]

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