Y chromosome palindromes and gene conversion

Abstract Muller’s ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller’s ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller’s ratchet to explore the evolution of the Y chromosome. The model assumes a non-recombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.

Download Full-text

Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome?: A Simulation Study

Genome Biology and Evolution ◽

10.1093/gbe/evq026 ◽

2010 ◽

Vol 2 (0) ◽

pp. 347-357 ◽

Cited By ~ 44

Author(s):

G. A. B. Marais ◽

P. R. A. Campos ◽

I. Gordo

Keyword(s):

Gene Conversion ◽

Y Chromosome ◽

Simulation Study ◽

Human Y Chromosome

Download Full-text

The degenerate Y chromosome – can conversion save it?

Reproduction Fertility and Development ◽

10.1071/rd03096 ◽

2004 ◽

Vol 16 (5) ◽

pp. 527 ◽

Cited By ~ 23

Author(s):

Jennifer A. Marshall Graves

Keyword(s):

Gene Conversion ◽

Y Chromosome ◽

Genetic Drift ◽

Sex Chromosome ◽

Chromosome Differentiation ◽

Y Chromosomes ◽

Speed Up ◽

Selection For ◽

Human Y Chromosome

The human Y chromosome is running out of time. In the last 300 million years, it has lost 1393 of its original 1438 genes, and at this rate it will lose the last 45 in a mere 10 million years. But there has been a proposal that perhaps rescue is at hand in the form of recently discovered gene conversion within palindromes. However, I argue here that although conversion will increase the frequency of variation of the Y (particularly amplification) between Y chromosomes in a population, it will not lead to a drive towards a more functional Y. The forces of evolution have made the Y a genetically isolated, non-recombining entity, vulnerable to genetic drift and selection for favourable new variants sharing the Y with damaging mutations. Perhaps it will even speed up the decline of the Y chromosome and the onset of a new round of sex-chromosome differentiation. The struggle to preserve males may perhaps lead to hominid speciation.

Download Full-text

Gene Duplication, Gene Conversion and the Evolution of the Y Chromosome

Genetics ◽

10.1534/genetics.110.116756 ◽

2010 ◽

Vol 186 (1) ◽

pp. 277-286 ◽

Cited By ~ 43

Author(s):

Tim Connallon ◽

Andrew G. Clark

Keyword(s):

Gene Duplication ◽

Gene Conversion ◽

Y Chromosome

Download Full-text

Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

10.1101/363101 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ching-Ho Chang ◽

Amanda M. Larracuente

Keyword(s):

Drosophila Melanogaster ◽

Gene Family ◽

Gene Conversion ◽

Y Chromosome ◽

Single Molecule ◽

De Novo ◽

High Rate ◽

Genome Wide ◽

Conversion Rates ◽

Multiple Copies

ABSTRACTHeterochromatic regions of the genome are repeat-rich and gene poor, and are therefore underrepresented in even in the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9-Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family—crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.

Download Full-text