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Molecular analysis of sex chromosome evolution in papaya

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Title: Molecular analysis of sex chromosome evolution in papaya
Author(s): Gschwend, Andrea
Director of Research: Ming, Ray
Doctoral Committee Chair(s): Ming, Ray
Doctoral Committee Member(s): Jacobs, Tom; Vodkin, Lila; Caetano-Anolles, Gustavo
Department / Program: Plant Biology
Discipline: Plant Biology
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(s): papaya Caricaceae sex chromosome evolution
Abstract: Sex chromosomes are of great interest due to their role in sexual reproduction. Sex chromosomes evolve through the suppression of recombination in the sex determining region between the X and Y chromosomes which allows for each region to evolve and change independently. Papaya’s trioecious sex is determined by a pair of incipient sex chromosomes. Papaya is the ideal species for studying sex chromosome evolution; it is trioecious, has a small sex determining region, and is in an early stage of sex chromosome evolution. To investigate the early consequences of sex chromosome evolution, the non-recombining regions of the nascent sex chromosomes of papaya were physically mapped, sequenced, annotated, and analyzed. The papaya hermaphrodite specific region of the Yh chromosome (HSY) is 8.1 megabases (Mb), larger than the 3.5 Mb corresponding region on the X chromosome, due mostly to an increase of retrotransposon insertions. Unlike the X, the HSY acquired genes from the autosome, a few of which have degenerated since they were obtained. Of the genes inherited from the ancestral chromosome, 46% have no functional copies on (and were therefore lost from) the HSY, and surprisingly, 29% were lost from the X. Thirty three HSY specific transcripts were identified, providing a list of sex determination gene candidates. This study provides the first detailed analysis of the sex-specific regions of a plant sex chromosome pair. Sex chromosomes evolve from an autosomal chromosome pair through suppression of recombination between the two. Though signs of Y evolution are distinct, with the expansion of the Y chromosome in early stages and the degeneration and loss of gene content, the X chromosome has long been thought to conserve the ancestral autosome’s structure and gene content. To determine whether the papaya X chromosome remained evolutionarily static and to compare the changes seen in the HSY and X regions to that of an outgroup, an orthologous autosomal region in Vasconcellea monoica, a monoecious relative in the family Caricaceae, was analyzed. Eleven V. monoica bacterial artificial chromosomes (BACs) corresponding to the X-specific region of papaya, and one V. monoica BAC corresponding to a papaya autosomal BAC, were sequenced, annotated, and analyzed. The papaya X-specific sequence was 133% larger than the V. monioica corresponding sequence, making the HSY sequence 5.4 times larger, supporting that both the HSY and X have expanded since their divergence from the ancestral autosome. The accumulation of retroelements contributed the most to the expansion, supporting the prediction of accumulation of transposable elements in the early stages of sex chromosome evolution. Both the X and the HSY have gained and lost genes and a gene rearrangement has occurred on the X, further supporting the conclusion that the X chromosome is not an unchanged version of the ancestral autosome. The sequencing of the papaya HSY and X sex-specific regions revealed a 4.6 Mb difference between the two sexes. Genome size differences have been detected between sexes in species with heteromorphic sex chromosomes using flow cytometry. I examined whether the 4.6 Mb difference between sexes can be detected using flow cytometry and tested whether a selection of dioecious and trioecious species in the family Caricaceae have detectable genome size difference between sexes. Nuclear DNA content for 11 of the 35 Caricaceae species was estimated using flow cytometry. Genome sizes were estimated for multiple sexes in seven of the 11 species. The papaya genome size was found to be 442.5 Mb, larger than previously predicted, and a 29% variation was seen across the average genome sizes of the 11 species. The 4.6 Mb difference could not accurately be detected using flow cytometry, but significant differences in genome size were detected between male and female samples in Jacaratia spinosa, Vasconcellea horovitziana, Vasconcellea parviflora, and Vasconcellea stipulata, and between male and hermaphrodite samples of Vasconcellea cundinamarcensis, suggesting the presence of sex chromosomes for these species. Vasconcellea horovitziana has a female genome size larger than the male, which was the opposite of what was expected and observed in the other Vasconcellea species, and would be interesting to explore further in the future. The results reported here support past hypotheses of early sex chromosome evolution, but the scale and pace of DNA sequence expansion in the HSY and in the X are surprising. The comparison between the HSY, X, and V. monoica sequence brought to light the new finding that the X region is also changing considerably, expanding as well and losing genes. It appears that papaya is not the only Caricaceae species that has evolved sex chromosomes; genome size differences between sexes suggest the dioecy seen in some Vasconcellea species and one Jacaratia species may be the result of independently evolved sex chromosomes, a finding that would be interesting to pursue in the future.
Issue Date: 2012-06-27
URI: http://hdl.handle.net/2142/31933
Rights Information: Chapter 1- copyright Nova Science Publishers 2012 Chapter 3- copyright PNAS 2012
Date Available in IDEALS: 2012-06-27
Date Deposited: 2012-05
 

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