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Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Sphyracephala beccarii Teleopsis quinqueguttata

PROVIDER: GSE75874 | GEO | 2015/12/11

SECONDARY ACCESSION(S): PRJNA305581

REPOSITORIES: GEO

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Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of 10 tissues into a grand transcriptome to identify genes located on the X and Y chromosomes of a stalk-eyed fly, Teleopsis dalmanni. We use next generation sequencing of RNA to identify over 500 genes that are differentially expressed in the testes due to the effects of a driving X chromosome (XSR) in T. dalmanni. Most of these genes were X-linked, evolving more rapidly than control genes, and exhibit elevated expression in the gonads. Finally, XSR has become genetically differentiated from standard X chromosomes – using the RNA sequence data, we found nearly 1000 sites in X-linked genes and only a handful in autosomal genes where there was a fixed nucleotide difference. We conclude that XSR has led to widespread sequence and expression divergence on the X chromosome in T. dalmanni.

2014-03-06 | GSE55601 | GEO

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

2015-12-11 | GSE75873 | GEO

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

2015-12-11 | GSE75872 | GEO

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of 10 tissues into a grand transcriptome to identify genes located on the X and Y chromosomes of a stalk-eyed fly, Teleopsis dalmanni. We use next generation sequencing of RNA to identify over 500 genes that are differentially expressed in the testes due to the effects of a driving X chromosome (XSR) in T. dalmanni. Most of these genes were X-linked, evolving more rapidly than control genes, and exhibit elevated expression in the gonads. Finally, XSR has become genetically differentiated from standard X chromosomes M-bM-^@M-^S using the RNA sequence data, we found nearly 1000 sites in X-linked genes and only a handful in autosomal genes where there was a fixed nucleotide difference. We conclude that XSR has led to widespread sequence and expression divergence on the X chromosome in T. dalmanni. Two-condition experiment, female vs. male DNA, for one species with 4 biological replicates

2014-03-06 | E-GEOD-55601 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-11 | E-GEOD-75874 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

2015-12-11 | E-GEOD-75873 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes. Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates

2015-12-11 | E-GEOD-75872 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis).

Project description:Chromosomal location has a significant effect on the evolutionary dynamics of genes involved in sexual dimorphism, impacting both the pattern of sex-specific gene expression and the rate of duplication and protein evolution for these genes. For nearly all non-model organisms, however, knowledge of chromosomal gene content is minimal and difficult to obtain on a genomic scale. In this study, we utilized Comparative Genomic Hybridization (CGH), using probes designed from EST sequence, to identify genes located on the X chromosome of four species in the stalk-eyed fly genus Teleopsis. Analysis of log(2) ratio values of female-to-male hybridization intensities from the CGH microarrays for over 3,400 genes reveals a strongly bimodal distribution that clearly differentiates autosomal from X-linked genes for all four species. Genotyping of 33 and linkage mapping of 28 of these genes in Teleopsis dalmanni indicate the CGH results correctly identified chromosomal location in all cases. Syntenic comparison with Drosophila indicates that 90% of the X-linked genes in Teleopsis are homologous to genes located on chromosome 2L in Drosophila melanogaster, suggesting the formation of a nearly complete neo-X chromosome from Muller element B in the dipteran lineage leading to Teleopsis. Analysis of gene movement both relative to Drosophila and within Teleopsis indicates that gene movement is significantly associated with 1) rates of protein evolution, 2) the pattern of gene duplication, and 3) the evolution of eyespan sexual dimorphism. Overall, this study reveals that diopsids are a critical group for understanding the evolution of sex chromosomes within Diptera. In addition, we demonstrate that CGH is a useful technique for identifying chromosomal sex-linkage and should be applicable to other organisms with EST or partial genomic information.

| S-EPMC2940734 | biostudies-literature

CGH reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis)

Project description:In this study, we utilized Comparative Genomic Hybridization (CGH), using probes designed from EST sequence, to identify genes located on the X chromosome of four species in the stalk-eyed fly genus Teleopsis. Analysis of log ratio values from the CGH microarrays for over 3400 genes produces a strongly bimodal distribution that clearly differentiates autosomal from X-linked genes for all four species. Genetic mapping of 35 of these genes in T. dalmanni indicates the CGH results correctly identified chromosomal location in all cases. Syntenic comparison with Drosophila indicates that 90% of the X-linked genes in Teleopsis are homologous to genes located on chromosome 2L in D. melanogaster, suggesting the formation of a nearly complete neo-X chromosome from Muller element B in the Dipteran lineage leading to Teleopsis. Overall, this study demonstrates CGH is a useful technique for identifying chromosomal sex-linkage and should be applicable to other organisms with EST or partial genomic information.

2010-03-01 | GSE20315 | GEO

CGH reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis)

2010-05-06 | E-GEOD-20315 | biostudies-arrayexpress