The pig X and Y chromosomes: structure, sequence and evolution

We have generated an improved assembly and gene annotation of the pig X chromosome, and a first draft assembly of the pig Y chromosome, by sequencing BAC and fosmid clones, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 of which are protein-coding. Gene order closely matches that found in Primates (including humans) and Carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X chromosome were absent from the pig (e.g. the cancer/testis antigen family) or inactive (e.g. AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on two clusters of male-specific low-copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. Many of the ancestral X-related genes previously reported in at least one mammalian Y chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes - both single copy and amplified - on the pig Y, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.

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Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

International Journal of Genomics ◽

10.1155/2013/261730 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 8

Author(s):

Ruth B. Phillips ◽

Jenefer J. DeKoning ◽

Joseph P. Brunelli ◽

Joshua J. Faber-Hammond ◽

John D. Hansen ◽

...

Keyword(s):

Rainbow Trout ◽

Candidate Genes ◽

Y Chromosome ◽

X Chromosome ◽

Bac Library ◽

Single Copy ◽

Bac Contig ◽

Protein Coding ◽

Additional Signal ◽

Male Specific

We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescencein situhybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

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Spot Urine for Sex Determination Forensic Identifications with Amelogenin Locus and Y chromosomes (DYS 19). Bercak Urin untuk Identifikasi Forensik Jenis Kelamin dengan Lokus Amelogenin dan Y Kromosom (DYS19)

Jurnal Biosains Pascasarjana ◽

10.20473/jbp.v20i3.2018.180-193 ◽

2018 ◽

Vol 20 (3) ◽

pp. 180

Author(s):

Yeti Eka Sispita Sari

Keyword(s):

Sex Determination ◽

Y Chromosome ◽

X Chromosome ◽

Sex Chromosome ◽

Dna Amplification ◽

Single Copy ◽

Amelogenin Gene ◽

Spot Urine ◽

Y Chromosomes ◽

Two Samples

AbstractBackground: Amelogenin gene was a single copy gene located in an X chromosome and a Y chromosome. The location of amelogenin gene for identification of sex chromosome has good variability between the form and the shape of the X chromosome and the Y chromosome and between Amelogenin alleles among different populations. Purpose: To prove urine spot examination on the results of the sex determination through Deoxyribo Nucleid Acid (DNA) isolation using amelogenin and Y chromosome loci (DYS19). Methods: Spotting the microscopic examination of urine samples to determine the presence or absence of urethral epithelial cells, followed by isolation Deoxyribo nucleid Acid (DNA) in order to determine the extent and purity of DNA amplification. Then performed Polymerase Chain Reaction (PCR) amelogenin locus at 106bp - 112bp and Y chromosomes (DYS19) at 232 -268 bp. Results: in 9 samples of men from 3 families with 3 kinship of different regions shows the results of different tests, because Amel Y variation between individual and populations method of determining the sex of 100% was inaccurate. In some men Amel Y can be removed entirely. This research should be visualized one band on the Y chromosome (DYS19) and the Amelogenin two bands during electrophoresis occurs misidentification of the sample as a woman. Conclusions: Identification of sex using Amelogenin locus and Y chromosomes (DYS19) has six identical and ambiguous results because the two samples shown as the sign of men but visualized as women, another sample was not visualized because of the thick level and concentration of Deoxyribo nucleid Acid (DNA).Keywords: Urine Spot, Sex Determination, Amelogenin, Y chromosome (DYS19).

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Muller’s ratchet of the Y chromosome with gene conversion

Genetics ◽

10.1093/genetics/iyab204 ◽

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.

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Analyzing and characterization of the chloroplast genome of Salix suchowensis

10.7287/peerj.preprints.2388 ◽

2016 ◽

Author(s):

Congrui Sun ◽

Jie Li ◽

Xiaogang Dai ◽

Yingnan Chen

Keyword(s):

Tandem Repeats ◽

Gene Annotation ◽

Repetitive Sequences ◽

Single Copy ◽

Phylogenetic Position ◽

Shrub Willow ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome ◽

Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

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Gene-level, but not chromosome-wide, divergence between a very young house fly proto-Y chromosome and its homologous proto-X chromosome

10.1101/2020.04.02.022707 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jae Hak Son ◽

Richard P. Meisel

Keyword(s):

Gene Expression ◽

Y Chromosome ◽

Chromosome Evolution ◽

Sex Chromosome ◽

House Fly ◽

Evolutionary Divergence ◽

Y Chromosomes ◽

Mitochondrial Functions ◽

Xx Males ◽

Y Chromosome Evolution

AbstractX and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene’s function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

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Mapping the mouse X chromosome: possible symmetry in the location of a family of sequences on the mouse X and Y chromosomes

Development ◽

10.1242/dev.101.supplement.107 ◽

1987 ◽

Vol 101 (Supplement) ◽

pp. 107-116

Author(s):

Philip Avner ◽

Colin Bishop ◽

Laurence Amar ◽

Jacques Cambrou ◽

Didier Hatat ◽

...

Keyword(s):

In Situ Hybridization ◽

Y Chromosome ◽

X Chromosome ◽

Somatic Cell Hybrid ◽

The Other ◽

Interspecific Crosses ◽

Somatic Cell Hybrid Panel ◽

Mus Spretus ◽

Y Chromosomes

Major advances in our knowledge of the genetic organization of the mouse X chromosome have been obtained by the use of interspecific crosses involving Mus spretus-derived strains. This system has been used to study sequences detected by three probes 80Y/B, 302Y/B and 371Y/B isolated from a mouse Y-chromosome library which have been shown to recognize both male–female common and male–female differential sequences. These patterns are due to the presence of a family of cross-reacting sequences on the mouse X and Y chromosomes. Detailed genetic analysis of the localization of the X-chromosomespecific sequences using both a somatic cell hybrid panel and an interspecific mouse cross has revealed the presence of at least three discrete clusters of loci (X–Y)A, (X–Y)B and (X–Y)C. Two of these clusters, (X–Y)B and (X–Y)C, lie distally on the mouse X chromosome, the other cluster (X–Y)A being situated close to the centromere. In situ hybridization shows a striking symmetry in the localization of the major sequences on both the X and Y chromosomes detected by these probes, hybridization being preferentially localized to a subcentromeric and subtelomeric region on each chromosome. This striking localization symmetry between the X and Y chromosome sequences is discussed in terms of the extensive pairing of the X–Y chromosomes noted during meiosis.

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Mapping the Y chromosome

Development ◽

10.1242/dev.101.supplement.39 ◽

1987 ◽

Vol 101 (Supplement) ◽

pp. 39-39

Author(s):

P. N. Goodfellow

Keyword(s):

Sex Determination ◽

Y Chromosome ◽

X Chromosome ◽

Dna Probes ◽

Genetic Maps ◽

Variable Amount ◽

Regional Localization ◽

Y Chromosomes ◽

Xx Males ◽

Human Y Chromosome

DNA probes isolated from the human Y chromosome have been used to resolve two fundamental problems concerning the biology of sex determination in man. Coincidentally, resolution of these problems has generated genetic maps of the short arm of the human Y chromosome and has allowed the regional localization of TDF. The first problem to be solved was the origin of XX males (de la Chapelle, this symposium): the majority of XX males are caused by a telomeric exchange between the X and Y chromosomes that results in TDF and a variable amount of Y-derived material being transferred to the X chromosome. The differing amounts of Y-derived material present in XX males has been used as the basis of a ‘deletion’ map of the Y chromosome (Müller; Ferguson-Smith & Affara; this symposium).

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Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

GigaScience ◽

10.1093/gigascience/giaa013 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 1

Author(s):

Xupo Ding ◽

Wenli Mei ◽

Qiang Lin ◽

Hao Wang ◽

Jun Wang ◽

...

Keyword(s):

Genome Assembly ◽

Gene Annotation ◽

Draft Genome ◽

Single Copy ◽

Aquilaria Sinensis ◽

Final Size ◽

Plant Resources ◽

Protein Coding ◽

High Level ◽

Chromosome Level

Abstract Backgroud Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. Findings We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18–84.37 million years ago. Conclusions Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.2062 ◽

2017 ◽

Vol 284 (1869) ◽

pp. 20172062 ◽

Cited By ~ 4

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.

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Molecular characterization of a mouse Y chromosomal repetitive sequence amplified in distantly related species in the genus Mus

Genome ◽

10.1139/g93-079 ◽

1993 ◽

Vol 36 (3) ◽

pp. 588-593 ◽

Cited By ~ 5

Author(s):

Yutaka Nishioka ◽

Becky M. Dolan ◽

Laila Zahed

Keyword(s):

Y Chromosome ◽

Repetitive Sequence ◽

Chromosome Evolution ◽

Fragment Length Polymorphism ◽

Gc Content ◽

Y Chromosomes ◽

Mouse Species ◽

Y Chromosome Evolution

This report describes a 1.1 kb long mouse Y chromosomal sequence designated 142-4. It has a 42% GC content and is rich in short direct and inverted repeats. 142-4 related sequences are repeated about 200 times in the Mus musculus Y chromosome and their distribution was visualized by in situ hybridization. 142-4 detected a restriction fragment length polymorphism that differentiated between the M. m. musculus type and the M. m. domesticus type Y chromosome. Southern blot analysis of DNAs isolated from a panel of mouse species showed that 142-4 related sequences were amplified in the Y chromosomes of M. minutoides, M. musculus, M. saxicola, M. spicilegus, and M. spretus but not in those of M. caroli, M. cookii, and M. pahari. These results suggest that 142-4 related sequences are evolutionary unstable and their accumulation patterns do not correlate with the known phylogenetic relationships of mouse species in the genus Mus.Key words: mouse Y chromosome, repetitive sequence, Mus, sequence amplification, Y chromosome evolution.

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