scholarly journals Y-chromosome structural diversity in the bonobo and chimpanzee lineages

2015 ◽  
Author(s):  
Matthew T. Oetjens ◽  
Feichen Shen ◽  
Sarah B. Emery ◽  
Zhengting Zou ◽  
Jeffrey M. Kidd
Keyword(s):  
Y Chromosome ◽  
Pan Troglodytes ◽  
Male Fertility ◽  
Copy Number ◽  
Tandem Repeats ◽  
Pan Paniscus ◽  
Genome Instability ◽  
Repetitive Sequences ◽  
Structural Diversity ◽  
Y Chromosomes

AbstractThe male specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem-repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four populations of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of speciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze 9 common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two bonobo (Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of azoospermia candidates RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.

scholarly journals Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shuang Wu ◽  
Jinyuan Chen ◽  
Ying Li ◽  
Ai Liu ◽  
Ao Li ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genome Instability ◽  
Repetitive Sequences ◽  
Genomic Analysis ◽  
Genomic Rearrangements ◽  
Comparative Genomic ◽  
Length Variation ◽  
Substitution Rates ◽  
Repeat Content ◽  
Plastome Evolution

Abstract Background Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. Results We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Conclusions Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.

scholarly journals The Y chromosome-linked copy number variations and male fertility

2011 ◽  
Vol 34 (5) ◽  
pp. 376-382 ◽  
Author(s):  
C. Krausz ◽  
C. Chianese ◽  
C. Giachini ◽  
E. Guarducci ◽  
I. Laface ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Male Fertility ◽  
Copy Number ◽  
Copy Number Variations

scholarly journals Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila

2021 ◽  
Author(s):  
Alison Nguyen ◽  
Doris Bachtrog
Keyword(s):  
Transposable Element ◽  
Y Chromosome ◽  
Structural Diversity ◽  
Size Difference ◽  
Drosophila Pseudoobscura ◽  
Nucleotide Variation ◽  
Y Chromosomes ◽  
Long Read ◽  
Low Levels ◽  
Element Accumulation

Y chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y chromosomes in D. pseudoobscura. We show that Y chromosomes differ by almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Ys. We show that Y chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. Intriguingly, the same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y chromosomes.

Y CHROMOSOME HYPERPLOIDY AND MALE FERTILITY IN DROSOPHILA MELANOGASTER

1979 ◽  
Vol 21 (1) ◽  
pp. 21-24 ◽  
Author(s):  
John H. Williamson ◽  
Eva Meidinger
Keyword(s):  
Drosophila Melanogaster ◽  
Y Chromosome ◽  
Mating Behavior ◽  
Male Fertility ◽  
Y Chromosomes

Drosophila melanogaster males with two supernumerary Y chromosomes, i.e. triplo-Y males, are completely sterile. Their mating behavior is normal, and spermatogenesis and spermiogenesis appear normal, but no sperm are transferred. Most, if not all, of the detrimental effects of a third Y chromosome on male fertility are attributable to the long arm of the Y chromosome.

scholarly journals Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain

2020 ◽  
Author(s):  
Gurdeep Matharu Lall ◽  
Maarten H. D. Larmuseau ◽  
Jon H. Wetton ◽  
Chiara Batini ◽  
Pille Hallast ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Tandem Repeats ◽  
Viking Age ◽  
British Isles ◽  
Administrative Control ◽  
Y Chromosomes ◽  
Male Specific ◽  
Demographic Impact ◽  
Specific Contribution ◽  
Short Tandem

Abstract The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.

scholarly journals Sex-specific adaptation and genomic responses to Y chromosome presence in female reproductive and neural tissues

2017 ◽  
Vol 284 (1869) ◽  
pp. 20172062 ◽  
Author(s):  
Alan T. Branco ◽  
Rute M Brito ◽  
Bernardo Lemos
Keyword(s):  
Y Chromosome ◽  
Repetitive Sequences ◽  
Reproductive Behaviour ◽  
Synaptic Function ◽  
Protein Coding ◽  
Specific Adaptation ◽  
Chromosome Addition ◽  
Y Chromosomes ◽  
Sexual Determination ◽  
Somatic Tissues

Y chromosomes typically harbour a small number of genes and an abundance of repetitive sequences. In Drosophila, the Y chromosome comprises multimegabase long segments of repetitive DNA and a handful of protein-coding genes. In mammals, the Y chromosome also harbours a disproportionally high abundance of repeats. Here, we built on a Drosophila melanogaster model in which the Y chromosome is decoupled from sexual determination. Genotypes were genetically identical for the autosomes, X chromosome, and mitochondria, but differ by the presence or dose of the Y chromosome. Addition of an extra Y chromosome had limited impact in males. However, the presence of a Y chromosome in females induced a disproportionate response in genes expressed in the ovaries as well as genes encoded by the mitochondrial genome. Furthermore, the data revealed significant consequences of Y chromosome presence in larvae neuronal tissue. This included the repression of genes implicated in reproductive behaviour, courtship, mating and synaptic function. Our findings exhibit the Y chromosome as a hotspot for sex-specific adaptation. They suggest roles for natural selection on Y-linked genetic elements exerting impact on sex-specific tissues as well as somatic tissues shared by males and females.

scholarly journals The Y chromosome of Drosophila melanogaster contains a distinctive subclass of Het-A-related repeats.

Genetics ◽  
1993 ◽  
Vol 134 (2) ◽  
pp. 531-543 ◽  
Author(s):  
O Danilevskaya ◽  
A Lofsky ◽  
E V Kurenova ◽  
M L Pardue
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Y Chromosome ◽  
Tandem Repeats ◽  
Chromosome Analysis ◽  
Sequence Identity ◽  
Y Chromosomes ◽  
Transposition Mechanism

Abstract The HeT-A element is a transposable element with an apparent role in the structure of the telomeres of Drosophila melanogaster chromosomes. HeT-A transposition is the earliest event detected in healing of broken ends; HeT-A is also found on telomeres of unbroken chromosomes. Sequences with homology to HeT-A are never detected in euchromatic regions; however, clusters of HeT-A-related sequences occur in nontelomeric regions of the heterochromatic Y chromosome. Analysis of two of these Y-associated clusters shows them to be significantly different in structure from telomeric HeT-A elements, although the regions of shared sequence have > 80% sequence identity in all cases. Telomeric HeT-A elements occur in chains, with the elements in the same orientation but variably truncated at their external ends and irregularly interspersed with unrelated sequences. In contrast, the nontelomeric Y elements are regular tandem repeats of parts of the HeT-A sequence joined to unrelated sequences which are not the same in the two clusters studied. The sequence structures suggest that the nontelomeric clusters on the Y chromosome do not arise by the same transposition mechanism that forms the telomeric clusters; instead the clusters on the Y may arise by a mechanism that is used more generally in the evolution of Y chromosomes. Although the telomeric and nontelomeric clusters appear to be formed differently, both are enriched in parts of the HeT-A sequence which may be important in the structure of heterochromatin.

Other genes of the Y chromosome

Development ◽  
1987 ◽  
Vol 101 (Supplement) ◽  
pp. 117-118
Author(s):  
Jonathan Wolfe
Keyword(s):  
Sex Determination ◽  
Y Chromosome ◽  
Male Fertility ◽  
Major Part ◽  
Essential Genes ◽  
Upper Limit ◽  
Y Chromosomes ◽  
Number Of Genes ◽  
The Moment ◽  
Human And Mouse

From the moment that the major part of the mammalian Y chromosome ceased to recombine with the X, the action of Muller's ratchet began to whittle away at it to remove all but the essential genes. Consequently, by comparison with their respective X homologues, both human and mouse Y chromosomes are relatively small and probably contain very few genes in a fabric of accumulated junk. Nevertheless, molecular biologists have not been deterred from searching for Y-linked genes and in recent years this has become an increasingly popular pastime. Although hard to find, any Y-linked genes are likely to play important roles in either sex determination or male fertility, a fact which has spurred the search. How many genes are likely to be present on the chromosome? If we accept the hypothesis that most genes are preceded by an HpaII tiny fragment (HTF) island, we can place an upper limit on the number of genes by considering the frequency with which such islands occur on the chromosome.

II. Distribution of DNA base sequences Sequence organization of the human Y chromosome

1978 ◽  
Vol 283 (997) ◽  
pp. 329-329
Keyword(s):  
Y Chromosome ◽  
Dna Hybridization ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Male And Female ◽  
Sequence Organization ◽  
Dna Base ◽  
Base Sequences ◽  
Specific Sequences ◽  
Human Y Chromosome

A comparison of restriction patterns of human male and female DNA after digestion with Hae III reveals two bands which are present only in male DNA and which are produced by cleavage of repetitive sequences found only on the human Y chromosome (Cooke 1976). Repetitive Y specific sequences can also be detected by exhaustive DNA/DNA hybridization (Kunkel, Smith & Boyer 1976). When DNA from one of these repetitive sequences is isolated as a fragment 3300 bases long from a Hae III digest of male DNA this material can be used as a probe for related sequences in male and female DNA. In both male and female DNA there is DNA which does not contain Hae III sites, which is complementary to this sequence and probably represents related tandem repeats. However, in male DNA fragments which are multiples of 3300 bases long are present showing that this sequence is tandemly repeated.

scholarly journals Site-specific transgenesis of the D. melanogaster Y-chromosome using CRISPR/Cas9

2018 ◽  
Author(s):  
Anna Buchman ◽  
Omar S. Akbari
Keyword(s):  
Y Chromosome ◽  
Repetitive Sequences ◽  
Chromosomal Translocations ◽  
Disease Vectors ◽  
Site Specific ◽  
Limited Success ◽  
Y Chromosomes ◽  
Landing Sites ◽  
Control Technologies ◽  
Random Insertion

AbstractDespite the importance of Y-chromosomes in evolution and sex determination, their heterochromatic, repeat-rich nature makes them difficult to sequence and genetically manipulate, and therefore they generally remain poorly understood. For example, the D. melanogaster Y-chromosome, one of the best understood, is widely heterochromatic and composed mainly of highly repetitive sequences, with only a handful of expressed genes scattered throughout its length. Efforts to insert transgenes on this chromosome have thus far relied on either random insertion of transposons (sometimes harboring ‘landing sites’ for subsequent integrations) with limited success or on chromosomal translocations, thereby limiting the types of Y-chromosome related questions that could be explored. Here we describe a versatile approach to site-specifically insert transgenes on the Y-chromosome in D. melanogaster via CRISPR/Cas9-mediated HDR. We demonstrate the ability to insert, and detect expression from, fluorescently marked transgenic transgenes at two specific locations on the Y-chromosome, and we utilize these marked Y-chromosomes to detect and quantify rare chromosomal nondisjunction effects. Finally, we discuss how this Y-docking technique could be adapted to other insects to aid in the development of genetic control technologies for the management of insect disease vectors and pests.

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