Date of Award

5-2008

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Legacy Department

Genetics and Biochemistry

Advisor

Abbott, Albert G

Abstract

Sex conferring chromosomes are subject to rapid change throughout evolution. Y-chromosomes (male determining) are subject to extensive chromatin remodeling and higher mutation rates than the autosomes being that recombination with the X chromosome is inhibited in many regions. The non-recombining regions comprise varying proportions of Y chromosomes from species to species and they are subject to mutation acquisition including both deletions and insertions. Recently it has been shown that these insertion mutations include repetitive DNA such as satellite DNA sequences (satDNA) and transposable elements. It is thought that Y chromosomes go through many rounds of expansion and contraction throughout evolution in a species and this may account for what seems to be homogenization of satDNA monomers that exist on Y chromosomes. In many species there is much evidence that satDNA is being homogenized through molecular turnover mechanisms and molecular drive.
Most plant Y chromosomes have been diverging for less time than those of animal Y chromosomes and therefore present an opportunity to study newly formed Y chromosomal constitutive heterochromatin. Plant Y chromosomes often posses more DNA content than their X counterparts. Furthermore, plant Y chromosomes seem to be lengthening while animal Y chromosomes appear to be in a state of diminution. These opposite growth states may be characteristic of young and old Y chromosomes respectively. It is reasonable to assume that the mechanisms causing the chromosomal dimorphism between X and Y chromosomes are the same throughout the genomes of various species, however, enhanced within non-recombining regions. Dissecting these molecular events can reveal some of the major forces and mechanisms driving evolution.
The sex system of Rumex acetosa (Sorrel) provides an ideal opportunity to study a recently evolved set of dimorphic sex chromosomes in plants. In this species, males have two Y chromosomes and a sex determination system resembling that of Drosophila. It has been estimated that the Y chromosomes of Sorrel started diverging from the X chromosomes ~15 million years ago and they contain approximately 57% more DNA content than the X chromosome.
It has been shown that much of the Y chromosomes are composed of constitutive heterochromatin and are rich in repetitive DNA. One such region is the Rumex acetosa Y specific repetitive satellite, RAYSI. Results by others show that tandem repeat arrays of RAYSI monomers are exclusive to the Y chromosomes and show a very low sequence diversity indicating high level of homogeneity amongst Y derived monomers.
It was suggested by Navajas et al. (2005) that RAYSI has evolved from a 120 bp sequence located autosomally. Until this study the evolution of the greater RAYSI family including monomers that are not from the Y-chromosomes. PCR based approaches of obtaining the RAYSI sequence have been utilized but until now none have observed the RAYSI tandem array in the original organization and genomic environment.
The following study investigates the composition, organization and origin of the greater RAYSI family, including non-Y monomers, and those from the Y tandem repeat arrays with particular emphasizes on revealing the constitutive heterochromatin environment in which it exists. Toward this goal RAYSI and its surrounding genomic environments were obtained in various ways. To obtain BAC sized heterochromatic regions from the Y chromosomes and putative X chromosomal regions a large insert BAC library of Sorrel was screened with the following probes; male enriched sequence probe RAYSI, probable X derived cDNA (RAXc4) and sex chromosome enriched satDNA probe (AAC)7. In order to obtain probable Y and X chromosome derived BACs. BACs were screened for Y chromosomal origin by hybridizing them as probes onto Southern blots of male and female genomic DNA. Four BACs from these experiments (two Y-derived RAYSI rich and two X-cDNA derived transcript rich) were partially sequenced revealing the DNA composition and arrangement of sequences within these genomic regions. BACs originating from the Y-chromosomes consist primarily of large tandem repeats of the RAYSI sequence and enrichment with the Ty3-gypsy retrotransposon. In contrast, BACs selected by hybridization with a probable X-derived cDNA, were depleted in these expanded sequences.
A phylogenetic study of RAYSI satDNA monomers from both male and female R. acetosa indicate a recent expansion of a derived RAYSI isoform on the Y chromosomes and the presence of ancestral isoforms that exist in both male and female genomes. In order to investigate the origins of the greater RAYSI family of sequences that have recently expanded on the Y chromosomes in arrays and the context of non-Y derived sequences, monomers derived from tandem, those putatively from the X chromosomes and perhaps autosomes were viewed on a scaled phylogram using R. crispus (as an outgroup). To characterize homogeneity of Y chromosomal RAYSI sequences and compare them to those from the X chromosomes (and perhaps autosomes), sequence diversity was estimated for various groups revealing the evolution of this particular satDNA that have helped to shape the constitutive heterochromatin regions of the R. Acetosa Y chromosomes. A derived variant of RAYSI has expanded into the tandem arrays that compose much of the constitutive heterochromatin of the Y chromosomes. This expansion may be directly responsible for the accumulation of DNA content evident in these recently evolved chromosomes. This derived form was the only isotype found on probable sex chromosome derived BACs suggesting that the homology found between X and Y chromosomal RAYSI sequences indicates recent common ancestry for these chromosomes.

Included in

Genetics Commons

Share

COinS