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59 results for “Sex Identification”
Fig. 2 in Identification of Sexually Dimorphic Genes in Pectoral Fin as Molecular Markers for Assessing the Sex of Japanese Silver Eels ().
Fig. 2. Comparisons of relative expression levels of six genes possibly higher expressed in the pectoral fins of female silver eels between the "S-Female" (n = 7, four repeats) and "S-Male" (n = 5, four repeats) groups. (A) LOC108249696, (B) LOC110515957, (C) egr3, (D) cipc, (E) LOC111853410, (F) cttn. The arp was a housekeeping gene, and two female samples (F1 and F2) were used as the internal control for calculating relative expression levels. The y-axis was in log2 scale. The "S-Female" meant the female silver eels, and the "S-Male" meant the male silver eels. The solid black line represented the median value, and the solid black circle represented the outliers. Asterisks indicated significant differences (**P <0.01, ***P <0.001) in relative expression levels between two groups.
Fig. 1 in Identification of Sexually Dimorphic Genes in Pectoral Fin as Molecular Markers for Assessing the Sex of Japanese Silver Eels ().
Fig. 1. Scheme of the MOLAS database for the Japanese eel. Annotated information of the assembled transcripts, including DNA sequence, amino acids sequence, open reading frames, signal peptides, transmembrane domains, gene ontology, hit KEGG pathway, and FPKM values, can be searched by the names of genes or the transcript ID in the Full-text search. A sequence of DNA can also be used to find the transcript with high similarity through the Sequence Search/BLAST. Moreover, the Pairwise Comparison can compare the differences in expression levels of the transcripts between two different libraries or two library groups, and then the differentially expressed genes can be summarized to a gene list. Furthermore, the Import Genelist can analyze the protein function, gene ontology enrichment, heatmap of expression, and hit terms on a KEGG pathway for a gene list. Additionally, the Clustering can be used to categorize the expressional patterns of transcripts between two different libraries or two library groups. Finally, the KEGG GlobalView and Gene List Analysis can see the hit terms of transcripts on the map of KEGG pathway and compare the different gene lists by Venn diagrams, respectively.
Dataset for Identification of giant hornet, Vespa mandarinia, queen sex pheromone components
<p>The Vespidae are a diverse family of wasps and hornets that contain invasive species and are formidable predators of insects, including social bees. Recently, the world’s largest hornet, <em>Vespa mandarinia</em> Smith(Hymenoptera: Vespidae), which occurs naturally in the Indomalayan region, has been found in Canada and United States. Some simulations indicate it could rapidly spread throughout Washington, Oregon, and parts of the eastern USA, threaten native bees and honey bees, and harm bee-pollinated crop production worth nearly $12 million annually. There is consequently an urgent need to learn more about <em>V. mandarinia</em>’s reproductive biology and to develop trapping methods to locate its nests and control its reproduction. We identified <em>V. mandarinia</em> queen-produced sex pheromone from the 5<sup>th</sup> and 6<sup>th</sup> intersegmental sternal glands of virgin queens. The major active compounds were hexanoic acid (HA), octanoic acid (OA) and decanoic acid (DA). When placed in field traps, the synthetic compounds and a queen-equivalent mixture rapidly attracted hundreds of males. This dataset provides the data used in this paper.</p>
Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds
<p><span>Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (<em>Corvus</em> <em>monedula</em>). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.</span></p>
Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds
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Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages
<p>Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.</p>
Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene
Genotypic sex identification assays can provide valuable information about fish populations when phenotypic sex determination is difficult. Here we describe the development of a TaqMan® assay (Ots_SexID) designed to identify the genotypic sex of Winter-Run Chinook salmon collected from the Sacramento River and spawned at the Livingston Stone National Fish Hatchery. The TaqMan® assay targets a region previously examined in the growth hormone pseudogene. Accuracy of the marker was assessed by comparing genotypic sex assignments for Chinook salmon spawned at Livingston Stone National Fish hatchery in 2012 (n = 84) to phenotypic sex recorded during spawning. Genotypic sex was observed to be concordant with phenotypic sex identified using Ots_SexID in 83/84 individuals, suggesting that the assay could be used to predict phenotypic sex with ~99% accuracy. To evaluate the utility of the TaqMan® assay in other parts of the species' range, we examined collections from 29 other populations ranging from Alaska to California. Sex assignments based on the assay were generally concordant with observed phenotypes, but there were some strong exceptions. These results suggest that the new assay will be very useful in Sacramento River Winter-Run Chinook salmon, but also highlight the importance of thoroughly testing any sex identification assay prior to application in a population of interest.
Data from: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene
Loci that can be used to screen for sex in salmon can provide important information for study of both wild and cultured populations. Here, we tested for associations between sex and genotypes at thousands of loci available from a genotyping-by-sequencing (GBS) dataset to discover sex-associated loci in sockeye salmon (Oncorhynchus nerka). We discovered seven sex-associated loci, developed high-throughput assays for two loci, and tested the utility of these two assays in eight collections of sockeye salmon sampled throughout North America. We also screened an existing assay based on the master sex-determining gene in salmon (sdY) in these collections. The ability of GBS-derived loci to assign fish to their phenotypic sex varied substantially among collections suggesting that recombination between the loci that we discovered and the sex-determining gene has occurred. Assignment accuracy to phenotypic sex was much higher with the sdY assay but was still less than 100%. Alignment of sequences from GBS-derived loci to draft genomes for two salmonids provided strong evidence that many of these loci are found on the chromosome orthologous to the known sex chromosome in sockeye salmon. Our study is the first to describe the approximate location of the sex-determining region in sockeye salmon and indicates that sdY is also the master sex-determining gene in this species. However, discordances between sdY genotypes and phenotypic sex and the variable performance of GBS-derived loci warrant more research.
Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
<p class="CxSpFirst">Atlantic cod (<i>Gadus morhua</i>,<i> </i>Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter spawning groups at specific regions of the genome. Guided regularized random forest and ranked <i>F</i><sub>ST</sub> methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.</p>
Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene
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Data from: Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers
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Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages
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Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
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Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures
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Data from: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene
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Data from: Identification of genomic regions associated with sex in Pacific halibut
Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing to identify RAD-tags that were linked to genetic sex, based on differentiation (FST) between the sexes. Identified RAD-tags were aligned to the Atlantic halibut (Hippoglossus hippoglossus) linkage map, the turbot (Scophthalmus maximus) genome, and the half-smooth tongue sole (Cynoglossus semilaevis) genome to identify genomic regions that may be involved in sex determination. In total, 56 RAD-tags (70 single nucleotide polymorphisms) were linked to sex, and three RAD-tags were identified in only females. Sex-linked loci aligned to three linkage groups in the Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), three chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1 locus), and one chromosome in the half-smooth tongue sole (ChrZ: 9 loci). Results add support to the hypothesis that Pacific halibut genetic sex is determined in a ZW system. Two sex-linked loci were further developed into sex identification assays, and their efficacy was tested on individuals that had been morphologically sexed. The accuracy of each assay on its own was 97.5% compared to morphological sex.
Data from: Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes
Fish have evolved a variety of sex-determining (SD) systems including male heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is known about SD mechanisms of Sebastes rockfishes, a highly speciose genus of importance to evolutionary and conservation biology. Here, we characterize the sex determination system in the sympatrically distributed sister species Sebastes chrysomelas and Sebastes carnatus. To identify sex-specific genotypic markers, double digest restriction site – associated DNA sequencing (ddRAD-seq) of genomic DNA from 40 sexed individuals of both species was performed. Loci were filtered for presence in all of the individuals of one sex, absence in the other sex and no heterozygosity. Of the 74 965 loci present in all males, 33 male-specific loci met the criteria in at least one species and 17 in both. Conversely, no female-specific loci were detected, together providing evidence of an XY sex determination system in both species. When aligned to a draft reference genome from Sebastes aleutianus, 26 sex-specific loci were interspersed among 1168 loci that were identical between sexes. The nascent Y chromosome averaged 5% divergence from the X chromosome and mapped to reference Sebastes genome scaffolds totalling 6.9Mbp in length. These scaffolds aligned to a single chromosome in three model fish genomes. Read coverage differences were also detected between sex-specific and autosomal loci. A PCR-RFLP assay validated the bioinformatic results and correctly identified sex of five additional individuals of known sex. A sex-determining gene in other teleosts gonadal soma-derived factor (gsdf) was present in the model fish chromosomes that spanned our sex-specific markers.
Data from: A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus)
In heterogametic species, biological differences between the two sexes are ubiquitous, and hence, errors in sex identification can be a significant source of noise and bias in studies where sex-related sources of variation are of interest or need to be controlled for. We developed and validated a universal multi-marker assay for reliable sex identification of three-spined sticklebacks (Gasterosteus aculeatus). The assay makes use of genotype scores from three sex-linked loci, and utilizes Bayesian probabilistic inference to identify sex of the genotyped individuals. The results, validated with 286 phenotypically sexed individuals from six populations of sticklebacks representing all major genetic lineages (cf. Pacific, Atlantic and Japan Sea) indicate that in contrast to commonly used single-marker based sex identification assays, the developed multi-marker assay should be 100% accurate. Since the markers in the assay can be scored from agarose gels, it provides a quick and cost-efficient tool for universal sex identification of three-spined sticklebacks. The general principle of combining information from multiple markers to improve the reliability of sex identification is transferable and can be utilized to develop and validate similar assays for other species.
Sex identification PCR-RFLP assay tested in eight species of Sebastes rockfish
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Data from: Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes
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