Abstract
The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9–8.4×10−4 events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages.
Highlights
The male-specific region of the human Y chromosome (MSY) is constitutively haploid, yet contains a high proportion (,35%) of pseudo-diploid duplicated regions, eight of which are arranged as large inverted repeats (‘palindromes’, known as P1 - P8; Figure 1a), with arms in most cases separated by non-duplicated spacers [1]
We investigated the details of a process that transfers sequence variants in one half of a palindrome into the other, thereby maintaining .99.9% similarity between the halves
Analysis of the chimpanzee and gorilla versions of the palindrome shows that the dynamic processes we see in human Y chromosomes have a deep evolutionary history
Summary
The male-specific region of the human Y chromosome (MSY) is constitutively haploid, yet contains a high proportion (,35%) of pseudo-diploid duplicated regions, eight of which are arranged as large inverted repeats (‘palindromes’, known as P1 - P8; Figure 1a), with arms in most cases separated by non-duplicated spacers [1]. It is becoming increasingly recognised that such palindromic structures are far from being a peculiarity of great ape Y chromosomes, but have more general biological significance as a feature of independently arising constitutively haploid sex chromosomes in other mammals [3,4,5], birds [6,7] and insects [8], as well as of the mammalian X chromosome [9,10], which is haploid in males Despite this general importance, and despite some theoretical analyses of palindrome evolution [11,12], little is known about the dynamics of conversion within these remarkable structures
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