scholarly journals Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
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.

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

2014 ◽  
Author(s):  
Benjamin M Skinner ◽  
Carole A Sargent ◽  
Carol Churcher ◽  
Toby Hunt ◽  
Javier Herrero ◽  
...  
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Gene Annotation ◽  
Olfactory Receptors ◽  
Single Copy ◽  
High Sequence Identity ◽  
Protein Coding ◽  
Sequencing Project ◽  
Y Chromosomes ◽  
Y Chromosome 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.

scholarly journals A Selective Sweep Associated With a Recent Gene Transposition in Drosophila miranda

Genetics ◽  
2000 ◽  
Vol 156 (4) ◽  
pp. 1753-1763 ◽  
Author(s):  
Soojin Yi ◽  
Brian Charlesworth
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Sequence Variation ◽  
Selective Sweep ◽  
Sex Chromosome ◽  
Selective Advantage ◽  
Chromosome Fusion ◽  
Gene Transposition ◽  
Sex Chromosome System ◽  
Male Specific

Abstract In Drosophila miranda, a chromosome fusion between the Y chromosome and the autosome corresponding to Muller’s element C has created a new sex chromosome system. The chromosome attached to the ancestral Y chromosome is transmitted paternally and hence is not exposed to crossing over. This chromosome, conventionally called the neo-Y, and the homologous neo-X chromosome display many properties of evolving sex chromosomes. We report here the transposition of the exuperantia1 (exu1) locus from a neo-sex chromosome to the ancestral X chromosome of D. miranda. Exu1 is known to have several critical developmental functions, including a male-specific role in spermatogenesis. The ancestral location of exu1 is conserved in the sibling species of D. miranda, as well as in a more distantly related species. The transposition of exu1 can be interpreted as an adaptive fixation, driven by a selective advantage conferred by its effect on dosage compensation. This explanation is supported by the pattern of within-species sequence variation at exu1 and the nearby exu2 locus. The implications of this phenomenon for genome evolution are discussed.

scholarly journals Similarities and differences of X and Y chromosome homologous genes, SRY and SOX3, in regulating the renin-angiotensin system promoters

2015 ◽  
Vol 47 (5) ◽  
pp. 177-186 ◽  
Author(s):  
Fabiano C. Araujo ◽  
Amy Milsted ◽  
Ingrid K. M. Watanabe ◽  
Helen L. Del Puerto ◽  
Robson A. S. Santos ◽  
...  
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Renin Angiotensin System ◽  
Male Rat ◽  
Rat Tissues ◽  
Angiotensin System ◽  
Renin Angiotensin ◽  
Rate Limiting Step ◽  
Chromosome Gene ◽  
Male Specific

The renin-angiotensin system (RAS) is subject to sex-specific modulation by hormones and gene products. However, sex differences in the balance between the vasoconstrictor/proliferative ACE/ANG II/AT1 axis, and the vasodilator/antiproliferative ACE2/ANG-(1–7)/MAS axis are poorly known. Data in the rat have suggested the male-specific Y-chromosome gene Sry to contribute to balance between these two axes, but why the testis-determining gene has these functions remains unknown. A combination of in silico genetic/protein comparisons, functional luciferase assays for promoters of the human RAS, and RNA-Seq profiling in rat were used to address if regulation of Sry on the RAS is conserved in the homologous X-chromosome gene, Sox3. Both SRY and SOX3 upregulated the promoter of Angiotensinogen ( AGT) and downregulated the promoters of ACE2, AT2, and MAS, likely through overlapping mechanisms. The regulation by both SRY and SOX3 on the MAS promoter indicates a cis regulation through multiple SOX binding sites. The Renin ( REN) promoter is upregulated by SRY and downregulated by SOX3, likely through trans and cis mechanisms, respectively. Sry transcripts are found in all analyzed male rat tissues including the kidney, while Sox3 transcripts are found only in the brain and testis, suggesting that the primary tissue for renin production (kidney) can only be regulated by SRY and not SOX3. These results suggest that SRY regulation of the RAS is partially shared with its X-chromosome homolog SOX3, but SRY gained a sex-specific control in the kidney for the rate-limiting step of the RAS, potentially resulting in male-specific blood pressure regulation.

scholarly journals 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)

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).

scholarly journals Enriched G-quadruplexes on the Drosophila Male X Chromosome Function as Insulators of Dosage Compensation Complex

2019 ◽  
Author(s):  
Sheng-Hu Qian ◽  
Lu Chen ◽  
Zhen-Xia Chen
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Binding Sites ◽  
Fine Tuning ◽  
Dosage Compensation Complex ◽  
Evolutionary Trajectory ◽  
Male Specific ◽  
Flanking Regions ◽  
Y Chromosome Degeneration

AbstractThe evolution of sex chromosomes has resulted in half X chromosome dosage in males as females. Dosage compensation, or the two-fold upregulation in males, was thus evolved to balance the gene expression between sexes. However, the step-wise evolutionary trajectory of dosage compensation during Y chromosome degeneration is still unclear. Here, we show that the specific structured elements G-quadruplexes (G4s) are enriched on the X chromosome in Drosophila melanogaster. Meanwhile, on the X chromosome, the G4s are underrepresented on the H4K16 acetylated regions and the binding sites of dosage compensation complex male-specific lethal (MSL) complex. Peaks of G4 density and potential are observed at the flanking regions of MSL binding sites, suggesting G4s act as insulators to precisely up-regulate certain regions in males. Thus, G4s may be involved in the evolution of dosage compensation process through fine-tuning one-dose proto-X chromosome regions around MSL binding sites during the gradual Y chromosome degeneration.One Sentence SummaryG-quadruplexes act as insulators to precisely up-regulate X chromosome in males.

Evolution of a Y Chromosome from an X Chromosome

2019 ◽  
Author(s):  
Roberta Bergero ◽  
Jim Gardner ◽  
Deborah Charlesworth
Keyword(s):  
Y Chromosome ◽  
X Chromosome

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1517
Author(s):  
Se-Hwan Cheon ◽  
Min-Ah Woo ◽  
Sangjin Jo ◽  
Young-Kee Kim ◽  
Ki-Joong Kim
Keyword(s):  
Northeast Asia ◽  
Single Copy ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Protein Coding ◽  
Tropical Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

scholarly journals Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pablo Cáceres ◽  
Agustín Barría ◽  
Kris A. Christensen ◽  
Liane N. Bassini ◽  
Katharina Correa ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Candidate Genes ◽  
Protein Phosphatase ◽  
Sea Lice ◽  
Genome Wide Association Studies ◽  
Dual Specificity ◽  
Dual Specificity Protein Phosphatase ◽  
Genomic Regions ◽  
Specificity Protein

AbstractSea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.

scholarly journals Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryoma Ota ◽  
Makoto Hayashi ◽  
Shumpei Morita ◽  
Hiroki Miura ◽  
Satoru Kobayashi
Keyword(s):  
X Chromosome ◽  
Germ Cells ◽  
Dosage Compensation ◽  
Sex Chromosome ◽  
Primordial Germ Cells ◽  
Histone H4 ◽  
X Chromosomes ◽  
Essential Components ◽  
Msl Complex ◽  
Male Specific

AbstractDosage compensation is a mechanism that equalizes sex chromosome gene expression between the sexes. In Drosophila, individuals with two X chromosomes (XX) become female, whereas males have one X chromosome (XY). In males, dosage compensation of the X chromosome in the soma is achieved by five proteins and two non-coding RNAs, which assemble into the male-specific lethal (MSL) complex to upregulate X-linked genes twofold. By contrast, it remains unclear whether dosage compensation occurs in the germline. To address this issue, we performed transcriptome analysis of male and female primordial germ cells (PGCs). We found that the expression levels of X-linked genes were approximately twofold higher in female PGCs than in male PGCs. Acetylation of lysine residue 16 on histone H4 (H4K16ac), which is catalyzed by the MSL complex, was undetectable in these cells. In male PGCs, hyperactivation of X-linked genes and H4K16ac were induced by overexpression of the essential components of the MSL complex, which were expressed at very low levels in PGCs. Together, these findings indicate that failure of MSL complex formation results in the absence of X-chromosome dosage compensation in male PGCs.

Sign in / Sign up

Export Citation Format

Share Document