Y-chromosome structural diversity in the bonobo and chimpanzee lineages

Oetjens, Matthew T.; Shen, Feichen; Emery, Sarah B.; Zou, Zhengting; Kidd, Jeffrey M.

doi:10.1101/029702

Cited by 2 publications

(7 citation statements)

References 80 publications

(122 reference statements)

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“…This is in contrast to other methods such as quantitative real-time PCR (qRT-PCR), in which suboptimal amplification efficiency influences cycle threshold values and can ultimately result in an inaccurate quantification of the target (Hindson et al 2011;McDermott et al 2013;Pinheiro et al 2012) . ddPCR was recently used to evaluate the copy number of ampliconic Y chromosome genes in humans and gorillas (Tomaszkiewicz et al 2016) and to verify computationally derived ampliconic gene copy number estimates for chimpanzees and bonobos (Oetjens et al 2016) .…”

Section: Resultsmentioning

confidence: 99%

“…Thus, almost each male analyzed had his own, unique haplotype. Previously, high levels of variation in ampliconic gene copy number were reported in chimpanzee and bonobo (Oetjens et al 2016) . Thus, our results are consistent with high levels of intrachromosomal rearrangements seen on the Y chromosome (Repping et al 2006) and with rapid evolution of Y chromosomal multi-copy genes (i.e.…”

Section: Discussionmentioning

confidence: 96%

“…Other groups have reported similar difficulties with TSPY. For example, a recent study (Oetjens et al 2016) used a k -mer based approach to detect ampliconic gene copy number variation in chimpanzees from whole-genome sequences. However, they found that the utility of their method for the repetitive TSPY array was limited, and their estimates of TSPY copy number included truncated gene copies (Oetjens et al 2016) .…”

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

“…For example, a recent study (Oetjens et al 2016) used a k -mer based approach to detect ampliconic gene copy number variation in chimpanzees from whole-genome sequences. However, they found that the utility of their method for the repetitive TSPY array was limited, and their estimates of TSPY copy number included truncated gene copies (Oetjens et al 2016) . Ghenu and colleagues were unable to develop a robust qPCR assay to analyze TSPY copy number in macaques (Ghenu et al 2016) .…”

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

“…Other groups have reported similar difficulties with TSPY. For example, a recent study conducted by Oetjens and colleagues (Oetjens et al 2016) used a k -mer based approach to detect ampliconic gene copy number variation in chimpanzees from whole-genome sequences.…”

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

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

Zaidi

Tomaszkiewicz

et al. 2017

Preprint

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Due to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis . Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups.Overall, only three gene families ( DAZ , RBMY , TSPY ) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual's height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 96%

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

Section: Potential Evolutionary Mechanisms and Other Factors Mutatiomentioning

confidence: 99%

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

Zaidi

Tomaszkiewicz

et al. 2017

Preprint

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The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

Makova,

Pickett,

Harris

et al. 2023

Preprint

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Apes possess two sex chromosomes—the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.

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Y-chromosome structural diversity in the bonobo and chimpanzee lineages

Cited by 2 publications

References 80 publications

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

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

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

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