High levels of copy number variation of ampliconic genes across major human Y haplogroups

Ye, Danling; Zaidi, Arslan; Tomaszkiewicz, Marta; Liebowitz, Corey; DeGiorgio, Michael; Shriver, Mark D.; Makova, Kateryna D.

doi:10.1101/230342

Cited by 4 publications

(5 citation statements)

References 72 publications

(123 reference statements)

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“…Bonobos nonwithstanding, Y-linked nucleotide variation is typically low in mammals (though, in contrast, copy number variation can sometimes highly polymorphic [Lucotte et al, 2017; Ye et al, 2017]). Y chromosome diversity is reported to be lower than neutral expectations in lynx, wolf, reindeer, cattle, and field vole (Hellborg and Ellegren 2004), and across Felidae (tiger, leopard, Asian leopard cat, fishing cat, Asian golden cat, and marbled cat; Luo et al.…”

Section: Mammalsmentioning

confidence: 99%

Genetic Diversity on the Sex Chromosomes

Sayres

2018

Genome Biology and Evolution

101

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Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.

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Section: Mammalsmentioning

confidence: 99%

Genetic Diversity on the Sex Chromosomes

Sayres

2018

Genome Biology and Evolution

101

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“…In polygynous mating systems, where a small proportion of males in the population mate with several females, the effective population size of the Y relative to the autosomes is smaller than that of the W (Mank, 2012;Wright & Mank, 2013). Relaxed purifying selection has been invoked to explain amplification of certain gene families on the primate and human Y chromosome, and the large variability in copy number across individuals and populations (Ghenu et al, 2016;Vegesna et al, 2020;Ye et al, 2018). Under drift, we expect variance in copy number to be approximately proportional to gene family size, where larger gene families will have a greater chance of gene duplication.…”

Section: Discussionmentioning

confidence: 99%

“…Why these ampliconic gene families have evolved on heteromorphic sex chromosomes is an open question and their phenotypic consequences remain debated. It is also becoming increasingly apparent that copy number of these gene families can vary substantially, not only across closely related species but also individuals of the same species (Brashear et al, 2018;Lucotte et al, 2018;Poznik et al, 2016;Vegesna et al, 2019;Vegesna et al, 2020;Ye et al, 2018). Understanding the factors driving this variability can provide insight into the adaptability and functional importance of sex chromosomes more broadly.…”

Section: Introductionmentioning

confidence: 99%

Multi-Copy Gene Family Evolution on the Avian W Chromosome

Rogers

Pizzari

Wright

2021

Journal of Heredity

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The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigate the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigate the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.

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“…It is this mechanism that can lead to gene copy number variations with resultant difficulties conceiving. Interestingly, even among healthy men there are variations in the Y amplionic gene copy number (30)(31)(32). Some of this variation is related to Y haplogroups, ethnicity, and geographic region, further complicating study of this phenomenon (32).…”

Section: The Y Chromosomementioning

confidence: 99%

“…Interestingly, even among healthy men there are variations in the Y amplionic gene copy number (30)(31)(32). Some of this variation is related to Y haplogroups, ethnicity, and geographic region, further complicating study of this phenomenon (32). This review will focus on CNV on the Y chromosome and how they play a role in male infertility and overall health.…”

Section: The Y Chromosomementioning

confidence: 99%

Y chromosome copy number variation and its effects on fertility and other health factors: a review

Rogers

2021

Transl Androl Urol

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The Y chromosome is essential for testis development and spermatogenesis. It is a chromosome with the lowest gene density owing to its medium size but paucity of coding genes. The Y chromosome is unique in that the majority of its structure is highly repetitive sequences, with the majority of these limited genes occurring in 9 amplionic sequences throughout the chromosome. The repetitive nature has its benefits as it can be protective against gene loss over many generations, but it can also predispose the Y chromosome to having wide variations of the number of gene copies present in these repeated sequences. This is known as copy number variation. Copy number variation is not unique to the Y chromosome but copy number variation is a well-known cause of male infertility and having effects on spermatogenesis. This is most commonly seen as deletions of the AZF sequences on the Y chromosome. However, there are other implications for copy number variation beyond just the AZF deletions that can affect spermatogenesis and potentially have other health implications. Copy number variations of TSPY1, DAZ, CDY1, RBMY1, the DYZ1 array, along with minor deletions of gr/gr, b1/b3, and b2/b3 have all be implicated in affecting spermatogenesis. UTY copy number variations have been implicated in risk for cardiovascular disease, and other deletions within gr/gr and the AZF sequences have been implicated in cancer and neuropsychiatric diseases. This review sets out to describe the Y chromosome and unique susceptibility to copy number variation and then to examine how this growing body of research impacts spermatogenesis and other health factors.

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High levels of copy number variation of ampliconic genes across major human Y haplogroups

Cited by 4 publications

References 72 publications

Genetic Diversity on the Sex Chromosomes

Genetic Diversity on the Sex Chromosomes

Multi-Copy Gene Family Evolution on the Avian W Chromosome

Y chromosome copy number variation and its effects on fertility and other health factors: a review

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