The Red Fox Y-Chromosome in Comparative Context

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Felis catus), dog (Canis lupus familiaris), and grey wolf (Canis lupus lupus), providing the opportunity to examine the red fox (Vulpes vulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.

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

10.1101/2021.08.16.456461 ◽

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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263 LABELING BOVINE SPERM Y-CHROMOSOME SEQUENCE USING DNA MIMICS

Reproduction Fertility and Development ◽

10.1071/rdv21n1ab263 ◽

2009 ◽

Vol 21 (1) ◽

pp. 229 ◽

Cited By ~ 3

Author(s):

B. A. Didion ◽

R. Bleher

Keyword(s):

Y Chromosome ◽

Somatic Cells ◽

Cell Nuclei ◽

Metaphase Chromosomes ◽

Synthetic Dna ◽

Bovine Sperm ◽

Hybridization Probes ◽

Y Chromosomes ◽

Chromosome Sequence ◽

In Situ Detection

Flow cytometric separation of X- and Y-chromosome bearing bovine sperm is an accepted technology for use at the commercial level. Nevertheless it is important to continue researching the area of gender-preselected sperm for improved efficiencies. We used a synthetic DNA mimic conjugated to a fluorescent dye for in situ detection of Y chromosomes in metaphase preparations of bovine somatic cells and spermatozoa. Peptide nucleic acids (PNA) are a type of DNA mimic having a higher affinity and stability than conventional DNA probes and are used as hybridization probes to complementary DNA. Using male bovine somatic cells and the Y-chromosome as a template, we arranged for the synthesis of a CY3-conjugated PNA to bind 13 to 15 base pairs of unique, Y-chromosome sequence. By testing different labeling conditions, we found that brief incubation (~1 h) of metaphase chromosomes with the PNA produced a localized signal on the Y-chromosome. No signals were observed when chromosomes of female bovine somatic cells were incubated with the same PNA probe. Because chromosomes occupy non-random territories in all cell nuclei, including sperm, we proposed to find centrally-located signals in 50% of fixed bovine sperm when treated with the same PNA as used for the somatic cells. As expected, we found the PNA signals present in 50% sperm (23/43) existing as a single, centrally-located, round fluorescent dot in the sperm head. Validation studies were also conducted using bovine sperm previously flow sorted into X or Y populations, and we found the signals in accordance to an expected signal present using the PNA (146/165 or 88.5% with PNA signal in presorted Y sperm heads and 13/174 or 7.5% with PNA signal in presorted X sperm heads).

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A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS

Life Science Alliance ◽

10.26508/lsa.202000902 ◽

2021 ◽

Vol 4 (4) ◽

pp. e202000902 ◽

Cited By ~ 1

Author(s):

Robert A Player ◽

Ellen R Forsyth ◽

Kathleen J Verratti ◽

David W Mohr ◽

Alan F Scott ◽

...

Keyword(s):

Canis Lupus ◽

Reference Genome ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Canis Lupus Familiaris ◽

High Molecular Weight Dna ◽

Short Read ◽

Genome Wide ◽

The Cost

Reference genome fidelity is critically important for genome wide association studies, yet most vary widely from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity. Further information is lost by economic necessity when genotyping populations, as lower resolution technologies such as genotyping arrays are commonly used. Here, we present a phased reference genome for Canis lupus familiaris using high molecular weight DNA-sequencing technologies. We tested wet laboratory and bioinformatic approaches to demonstrate a minimum workflow to generate the 2.4 gigabase genome for a Labrador Retriever. The de novo assembly required eight Oxford Nanopore R9.4 flowcells (∼23X depth) and running a 10X Genomics library on the equivalent of one lane of an Illumina NovaSeq S1 flowcell (∼88X depth), bringing the cost of generating a nearly complete reference genome to less than $10K (USD). Mapping of short-read data from 10 Labrador Retrievers against this reference resulted in 1% more aligned reads versus the current reference (CanFam3.1, P < 0.001), and a 15% reduction of variant calls, increasing the chance of identifying true, low-effect size variants in a genome-wide association studies. We believe that by incorporating the cost to produce a full genome assembly into any large-scale genotyping project, an investigator can improve study power, decrease costs, and optimize the overall scientific value of their study.

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Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome

PLoS Genetics ◽

10.1371/journal.pgen.1009438 ◽

2021 ◽

Vol 17 (4) ◽

pp. e1009438

Author(s):

Alison H. Nguyen ◽

Doris Bachtrog

Keyword(s):

Y Chromosome ◽

Sex Chromosomes ◽

Young Male ◽

Heterochromatin Formation ◽

Young Males ◽

Repeat Content ◽

Y Chromosomes ◽

Active Transcription ◽

Heterogametic Sex ◽

Effects Of Aging

Sex-specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well-assembled young Y chromosome of Drosophila miranda to study the sex-specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de-repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the TE-rich neo-Y chromosome, presumably due to active transcription of a large number of neo-Y linked genes, resulting in up-regulation of Y-linked TEs already in young males. This is consistent with an interaction between the evolutionary age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that “toxic Y chromosomes” can diminish male fitness and a reduction in heterochromatin can contribute to sex-specific aging.

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The good, the bad, and the ugly: space use and intraguild interactions among three opportunistic predators—cat (Felis catus), dog (Canis lupus familiaris), and red fox (Vulpes vulpes)—under human pressure

Canadian Journal of Zoology ◽

10.1139/cjz-2012-0072 ◽

2012 ◽

Vol 90 (12) ◽

pp. 1402-1413 ◽

Cited By ~ 36

Author(s):

D. Krauze-Gryz ◽

J.B. Gryz ◽

J. Goszczyński ◽

P. Chylarecki ◽

M. ̇Zmihorski

Keyword(s):

Canis Lupus ◽

Vulpes Vulpes ◽

Red Fox ◽

Space Use ◽

Felis Catus ◽

Probability Of Detection ◽

The Other ◽

Canis Lupus Familiaris ◽

Modeling Framework ◽

Intraguild Interactions

Examples of interspecific interactions have been described for mammalian predators, but less is known regarding disturbances of native predator guilds by domestic predators. We investigated intraguild interactions among three opportunistic predators (dog ( Canis lupus familiaris L., 1758), cat ( Felis catus L., 1758), and red fox ( Vulpes vulpes (L., 1758)) co-occurring in the extensive farmlands of central Poland. Their space use was monitored using tracking stations distributed in field and forest plots along a distance gradient from buildings and analyzed using the occupancy-modeling framework. For all three species occupancy decreased with increased distance from buildings, although for the fox the pattern was relatively weak. The occurrence of cats at the stations was higher in the forest than in the field; for fox and dog, there was a strong variation between study plots. For all three predators, the probability of detection was higher during the night than during the day and varied between the seasons; however, the exact patterns were species-specific. The presence of one predator was also linked to the presence of the other two species—generally, a given species was detected more frequently in the absence of the other two species. We recorded spatiotemporal niche segregation among the three species. We conclude that interspecific antagonistic interactions and differences in foraging ecology are the main drivers shaping co-occurrence of the three species in the agriculture landscape.

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

eLife ◽

10.7554/elife.75795 ◽

2022 ◽

Vol 11 ◽

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

Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, 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 contributes to the convergent evolution of Y chromosome organization across organisms.

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A Phased Canis lupus familiaris Labrador Retriever Reference Genome Utilizing High Molecular Weight DNA Extraction Methods and High Resolution Sequencing Technologies

10.1101/2020.08.26.269076 ◽

2020 ◽

Author(s):

Robert A. Player ◽

Ellen R. Forsyth ◽

Kathleen J. Verratti ◽

David W. Mohr ◽

Alan F. Scott ◽

...

Keyword(s):

Molecular Weight ◽

High Molecular Weight ◽

Canis Lupus ◽

Reference Genome ◽

Labrador Retriever ◽

Specific Reference ◽

Canis Lupus Familiaris ◽

Short Read ◽

Sequencing Technologies ◽

The Cost

ABSTRACTReference genome fidelity is critically important for genome wide association studies (GWAS), yet many are incomplete or too dissimilar from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity low complexity. Further information is lost by economic necessity when genotyping populations, as lower resolution technologies such as genotyping arrays are commonly utilized. Here we present a phased reference genome for Canis lupus familiaris utilizing high molecular weight sequencing technologies. We tested wet lab and bioinformatic approaches to demonstrate a minimum workflow to generate the 2.4 gigabase genome for a Labrador Retriever. The resulting de novo assembly required eight Oxford Nanopore R9.4 flowcells (~23X depth) and running a 10X Genomics library on the equivalent of one lane of an Illumina NovaSeq S1 flowcell (~88X depth), bringing the cost of generating a nearly complete reference genome to less than $10K. Mapping of publicly available short-read data from ten Labrador Retrievers against this breed-specific reference resulted in an average of approximately 1% more aligned reads compared to mapping against the current gold standard reference (CanFam3.1, p<0.001), indicating a more complete breed-specific reference. An average 15% reduction of variant calls was observed from the same mapped data, which increases the chance of identifying low effect size variants in a GWAS. We believe that by incorporating the cost to produce a full genome assembly into any large-scale canine genotyping study, an investigator can make an informed cost/benefit analysis regarding genotyping technology.

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

10.1101/058412 ◽

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.

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Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome

10.1101/2020.07.21.214528 ◽

2020 ◽

Cited By ~ 2

Author(s):

Alison H. Nguyen ◽

Doris Bachtrog

Keyword(s):

Y Chromosome ◽

Sex Chromosomes ◽

Young Male ◽

Heterochromatin Formation ◽

Young Males ◽

Repeat Content ◽

Y Chromosomes ◽

Heteromorphic Sex Chromosomes ◽

Heterogametic Sex ◽

Effects Of Aging

Sex‐specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well‐assembled young Y chromosome of Drosophila miranda to study the sex‐specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de‐repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the large TE‐ rich neo‐Y chromosome, resulting in up‐regulation of Y‐linked TEs already in young males. This is consistent with an interaction between the age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that “toxic Y chromosomes” can diminish male fitness and a reduction in heterochromatin can contribute to sex‐specific aging.

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Selective single molecule sequencing and assembly of a human Y chromosome of African origin

10.1101/342667 ◽

2018 ◽

Cited By ~ 1

Author(s):

Lukas F.K. Kuderna ◽

Esther Lizano ◽

Eva Julià ◽

Jessica Gomez-Garrido ◽

Aitor Serres-Armero ◽

...

Keyword(s):

Y Chromosome ◽

Single Molecule ◽

Genomic Analysis ◽

European Ancestry ◽

African Origin ◽

Repeat Content ◽

Y Chromosomes ◽

Reference Quality ◽

Novel Strategy ◽

Human Y Chromosome

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions1, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology2–5. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous and complete assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%6, thus allowing a chromosome scale analysis of human Y chromosomes. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ7. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.

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