scholarly journals SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms

2016 ◽  
Vol 8 (8) ◽  
pp. 2530-2543 ◽  
Author(s):  
Aline Muyle ◽  
Jos Käfer ◽  
Niklaus Zemp ◽  
Sylvain Mousset ◽  
Franck Picard ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Probabilistic Approach ◽  
Model Organisms

scholarly journals SEX-DETector: a probabilistic approach to uncover sex chromosomes in non-model organisms

2015 ◽  
Author(s):  
Aline Muyle ◽  
Jos Käfer ◽  
Niklaus Zemp ◽  
Sylvain Mousset ◽  
Franck Picard ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Model Comparison ◽  
Sex Chromosome ◽  
A Priori ◽  
Probabilistic Approach ◽  
Model Organisms ◽  
Rna Seq ◽  
A Genome ◽  
Cost Efficient ◽  
Sex Determination System

AbstractData deposition: During the review process, the SEX-DETector galaxy workflow and associated test datasets are made available on the public galaxy.prabi.fr server. The data as well as the tool interface are visible to anonymous users, but to use them, you should register for an account (“user Register”), and import the data library “SEX-DETector” (“Shared Data Data Libraries”) into your history. More instructions can be found in the “readme” file in this library. The user manual for SEX-DETector is available here: https://lbbe.univ-lyon1.fr/Download-5251.html?lang=en.Paper submitted as a Genome Resource.We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, UV). Sex chromosomes (especially the nonrecombining and repeat-dense Y, W, U and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. However, most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical data show that our method identifies many more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Simulations suggest few individuals are needed for optimal results. For species with unknown sex-determination system, the method can assess the presence and type (XY versus ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimised for sex chomosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organism, including non-model ones for which nothing is known a priori, that can be bred in the lab, is suitable for our method. SEX-DETector is made freely available to the community through a Galaxy workflow.

scholarly journals Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera

2021 ◽  
Vol 376 (1833) ◽  
pp. 20200101
Author(s):  
Basanta Bista ◽  
Zhiqiang Wu ◽  
Robert Literman ◽  
Nicole Valenzuela
Keyword(s):  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Context Effects ◽  
Model Organisms ◽  
Transcriptional Networks ◽  
Type I ◽  
Gene Dose ◽  
Type Iv ◽  
Apalone Spinifera

Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone 's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone 's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

scholarly journals dCAPS method: advantages, troubles and solution

2008 ◽  
Vol 53 (No. 9) ◽  
pp. 417-420 ◽  
Author(s):  
M. Hrubá
Keyword(s):  
Genetic Mapping ◽  
Sex Chromosomes ◽  
Restriction Site ◽  
Cost Effective ◽  
Fundamental Principle ◽  
The Other ◽  
Model Organisms ◽  
Target Sequence ◽  
Evolutionary Studies ◽  
Sequence Polymorphisms

In our work, we focus on the evolutionary studies of sex chromosomes. As model organisms we use several species of the plant genus <i>Silene</i>. An important part of our research is represented by genetic mapping based on the assays of DNA length or sequence polymorphisms. Apart from the other methods we also use the dCAPS method, which is very useful for detection of the sequence polymorphisms (SNPs). This method is unique as it is able to detect SNPs that are not situated in any restriction site; a fundamental principle of this method is usage of primer designed with one or two mismatches that bring into the target sequence the mutation in vicinity of SNP. Using this method, we found out some improvements that can make analyses more cost-effective.

scholarly journals Identification of the homozygotic sex chromosome of non-model organisms

2021 ◽  
Author(s):  
Charles Christian Hansen ◽  
Kristen Westfall ◽  
Snaebjorn Palsson
Keyword(s):  
Sex Chromosomes ◽  
Reference Genome ◽  
Sex Chromosome ◽  
Read Depth ◽  
Genomic Variation ◽  
Model Organisms ◽  
Z Chromosome ◽  
Organelle Genomes ◽  
Whole Genomes ◽  
Heterogametic Sex

Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes and, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types can have highly disparate evolutionary histories, it is imperative to take this information into account when analyzing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome using two whole genome sequenced (WGS) and 133 RAD sequenced white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold, ii) heterozygosity per scaffold in a male and female bird, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) an analysis of SNP-loadings from a principal components analysis (PCA), based on low-depth RADseq data from 133 individuals. In i and ii, the WGS were mapped to a reference genome consisting of 1142 assembled scaffolds from the golden eagle (Aquila chrysaetos) with no identified chromosomes. The read depth per scaffold identified 86.41% of the homogametic sex chromosome (Z) with few false positives. The SNP-loading scores found 78.6% of the Z-chromosome but had a false positive discovery rate of more than 10%. The heterozygosity per scaffold did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W).

scholarly journals Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

2019 ◽  
Vol 9 (10) ◽  
pp. 3467-3476 ◽  
Author(s):  
Paul M. Hime ◽  
Jeffrey T. Briggler ◽  
Joshua S. Reece ◽  
David W. Weisrock
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Model Organisms ◽  
Reduced Representation ◽  
Non Invasive ◽  
Female Heterogamety ◽  
Genome Wide ◽  
Great Utility ◽  
Genomic Regions

Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.

Reductionist thinking and animal models in neuropsychiatric research

2019 ◽  
Vol 42 ◽  
Author(s):  
Nicole M. Baran
Keyword(s):  
Animal Models ◽  
Mental Disorders ◽  
Environmental Factors ◽  
Neuropsychiatric Disorders ◽  
Model Organisms ◽  
Developmental Genetic ◽  
Term Study ◽  
Genetic And Environmental Factors ◽  
Mechanisms Of Plasticity

AbstractReductionist thinking in neuroscience is manifest in the widespread use of animal models of neuropsychiatric disorders. Broader investigations of diverse behaviors in non-model organisms and longer-term study of the mechanisms of plasticity will yield fundamental insights into the neurobiological, developmental, genetic, and environmental factors contributing to the “massively multifactorial system networks” which go awry in mental disorders.

Apoptosis and development

2003 ◽  
Vol 39 ◽  
pp. 11-24 ◽  
Author(s):  
Justin V McCarthy
Keyword(s):  
Drosophila Melanogaster ◽  
Mammalian Cells ◽  
Cell Number ◽  
Model Organisms ◽  
Biological Processes ◽  
Nematode Caenorhabditis Elegans ◽  
Apoptotic Pathway ◽  
Genetic Pathways ◽  
Evolutionarily Conserved ◽  
Multicellular Organisms

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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