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.

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.

scholarly journals Structural changes following the reversal of a Y Chromosome to an autosome in Drosophila pseudoobscura

2016 ◽  
Author(s):  
Ching-Ho Chang ◽  
Amanda M. Larracuente
Keyword(s):  
Y Chromosome ◽  
Single Molecule ◽  
Sex Chromosomes ◽  
Structural Changes ◽  
Drosophila Pseudoobscura ◽  
X Chromosomes ◽  
Repeat Content ◽  
Y Chromosomes ◽  
Rapid Sequence ◽  
Compact Size

AbstractRobertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution in animals by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given that autosomes and sex chromosomes differ in gene regulation and chromatin environment. While researchers are beginning to understand X chromosomes reversals to autosomes at a genomic level, it is difficult to study reversals of Y chromosomes because of their rapid sequence turnover and high repeat content. To gain insight into the genomic events following a Y chromosome reversal, we investigated an autosome-Y translocation in a well-studied and tractable organism, Drosophila pseudoobscura. About 10-15 Mya, the ancestral Y chromosome fused to a small autosome (the dot chromosome) in an ancestor of D. pseudoobscura. We used single molecule real-time sequencing reads to assemble the genic part of the D. pseudoobscura dot chromosome, including this Y-to-dot translocation. We find that the intervening sequence between the ancestral Y and the rest of the dot chromosome is only ~78 Kb and has a low repeat density, suggesting that the centromere now falls outside, rather than between, the fused chromosomes. The Y-to-dot region is 100 times smaller than the D. melanogaster Y chromosome, owing to repeat landscape changes. Previous studies suggest that recurrent selective sweeps favoring shorter introns helped to shrink the Y-to-dot following the translocation. Our results suggest that genetic drift and a small ancestral Y chromosome may also help explain the compact size of the Y-to-dot translocation.

scholarly journals Assembly of a young vertebrate Y chromosome reveals convergent signatures of sex chromosome evolution

2019 ◽  
Author(s):  
Catherine L. Peichel ◽  
Shaugnessy R. McCann ◽  
Joseph A. Ross ◽  
Alice F. S. Naftaly ◽  
James R. Urton ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Gasterosteus Aculeatus ◽  
Sex Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Threespine Stickleback ◽  
Evolutionary Forces ◽  
Y Chromosomes ◽  
Long Read

AbstractHeteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to rapid degeneration of the Y chromosome. However, these early stages of degeneration are not well understood, as complete Y chromosome sequence assemblies have only been generated across a handful of taxa with ancient sex chromosomes. Here we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old. Our previous work identified that the non-recombining region between the X and the Y spans ∼17.5 Mb on the X chromosome. Here, we combined long-read PacBio sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome clones from a bacterial artificial chromosome (BAC) library. We found three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The young threespine stickleback Y shows convergence with older sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we found no evidence for large amplicons found in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). Together, our work shows that the same evolutionary forces shaping older sex chromosomes can cause remarkably rapid changes in the overall genetic architecture on young Y chromosomes.

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 An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 105
Author(s):  
Matthew J. Jevit ◽  
Brian W. Davis ◽  
Caitlin Castaneda ◽  
Andrew Hillhouse ◽  
Rytis Juras ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Complex Structure ◽  
Pseudoautosomal Region ◽  
Final Assembly ◽  
Y Chromosomes ◽  
Vicugna Pacos ◽  
Starting Point ◽  
Long Read

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

scholarly journals Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingzhan Xue ◽  
Yu Gao ◽  
Meiying Wu ◽  
Tian Tian ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Sex Chromosome ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Recent Origin ◽  
Mastacembelus Armatus

Abstract Background The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Conclusions Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

Muller’s ratchet of the Y chromosome with gene conversion

Genetics ◽  
2021 ◽  
Author(s):  
Takahiro Sakamoto ◽  
Hideki Innan
Keyword(s):  
Gene Duplication ◽  
Gene Conversion ◽  
Y Chromosome ◽  
Conversion Rate ◽  
Single Copy ◽  
Duplicated Genes ◽  
Fitness Effect ◽  
Muller's Ratchet ◽  
Y Chromosomes ◽  
Muller’S Ratchet

Abstract Muller’s ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller’s ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller’s ratchet to explore the evolution of the Y chromosome. The model assumes a non-recombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

2021 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E. Gregory ◽  
Kathleen E. Gordon ◽  
Colin D. Meiklejohn ◽  
Amanda M. Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

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