scholarly journals Expansion of the HSFY gene family in pig lineages

2014 ◽  
Author(s):  
Benjamin M Skinner ◽  
Kim Lachani ◽  
Carole A Sargent ◽  
Fengtang Yang ◽  
Peter JI Ellis ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Bos Taurus ◽  
Mammalian Species ◽  
Gene Copy Number ◽  
Gene Families ◽  
Gene Copy ◽  
Biological Functions ◽  
Domestic Pig ◽  
Nonsense Mutations

Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. The HSFY family has amplified on the Y chromosome of the domestic pig (Sus scrofa), in an apparently independent event to an HSFY expansion on the Y chromosome of cattle (Bos taurus). Although the biological functions of HSFY genes are poorly understood, they appear to be involved in gametogenesis in a number of mammalian species, and, in cattle, HSFY gene copy number correlates with levels of fertility. We have investigated the HSFY family in domestic pigs, and other suid species including warthogs, bushpigs, babirusas and peccaries. The domestic pig contains at least two amplified variants of HSFY, distinguished predominantly by presence or absence of a SINE within the intron. Both these variants are expressed in testis, and both are present in approximately 50 copies each in a single cluster on the short arm of the Y. The longer form has multiple nonsense mutations rendering it likely non-functional, but many of the shorter forms still have coding potential. Other suid species also have these two variants of HSFY, and estimates of copy number suggest the HSFY family may have amplified independently twice during suid evolution. Given the association of HSFY gene copy number with fertility in cattle, HSFY is likely to play an important role in spermatogenesis in pigs also.

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

2017 ◽  
Author(s):  
Danling Ye ◽  
Arslan Zaidi ◽  
Marta Tomaszkiewicz ◽  
Corey Liebowitz ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Families ◽  
Digital Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

AbstractDue 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 (DATZ, 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.

scholarly journals Y chromosome gene copy number and lack of autism phenotype in a male with an isodicentric Y chromosome and absent NLGN4Y expression

2019 ◽  
Vol 180 (7) ◽  
pp. 471-482 ◽  
Author(s):  
Judith L. Ross ◽  
Luke Bloy ◽  
Timothy P. L. Roberts ◽  
Judith Miller ◽  
Chao Xing ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Chromosome Gene ◽  
Autism Phenotype

scholarly journals Amylasecopy number analysis in several mammalian lineages reveals convergent adaptive bursts shaped by diet

2018 ◽  
Author(s):  
Petar Pajic ◽  
Pavlos Pavlidis ◽  
Kirsten Dean ◽  
Lubov Neznanova ◽  
Erin Daugherity ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Copy Number ◽  
Mammalian Species ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Adaptive Mechanism ◽  
Amylase Gene ◽  
Present Evidence ◽  
Copy Number Amplification

AbstractThe amylase gene (AMY), which codes for a starch-digesting enzyme in animals, underwent several gene copy number gains in humans1, dogs2, and mice3, presumably along with increased starch consumption during the evolution of these species. Here we present evidence for additionalAMYcopy number expansions in several mammalian species, most of which also consume starch-rich diets. We also show that these independentAMYcopy number gains are often accompanied by a gain in enzymatic activity of amylase in saliva. We used multi-species coalescent modeling to provide further evidence that these recurrentAMYgene copy number expansions were adaptive. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast adaptive mechanism in evolution that can independently occur in different branches of the phylogeny.

scholarly journals Independent amylase gene copy number bursts correlate with dietary preferences in mammals

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Petar Pajic ◽  
Pavlos Pavlidis ◽  
Kirsten Dean ◽  
Lubov Neznanova ◽  
Rose-Anne Romano ◽  
...  
Keyword(s):  
Copy Number ◽  
Mammalian Species ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Duplications ◽  
Amylase Gene ◽  
Evolutionary Mechanism ◽  
Dietary Preferences ◽  
Copy Number Amplification

The amylase gene (AMY), which codes for a starch-digesting enzyme in animals, underwent several gene copy number gains in humans (Perry et al., 2007), dogs (Axelsson et al., 2013), and mice (Schibler et al., 1982), possibly along with increased starch consumption during the evolution of these species. Here, we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny.

scholarly journals Copy Number Lability and Evolutionary Dynamics of the Adh Gene Family in Diploid and Tetraploid Cotton (Gossypium)

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1913-1926 ◽  
Author(s):  
Randall L Small ◽  
Jonathan F Wendel
Keyword(s):  
Gene Family ◽  
Copy Number ◽  
Evolutionary Dynamics ◽  
Gene Copy Number ◽  
Nuclear Gene ◽  
Gene Families ◽  
Gene Copy ◽  
Tetraploid Cotton ◽  
Gossypium Species ◽  
Adh Gene

Abstract Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.

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