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.
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
Project description:Phylogenetic relationships in Dendrosenecio
Project description:<p>Harmful algal blooms (HABs) of the toxic haptophyte <em>Prymnesium parvum</em> are a recurrent problem in many inland and estuarine waters around the world. Strains of <em>P. parvum</em> vary in the toxins they produce and in other physiological traits associated with HABs, but the genetic basis for this variation is unknown. To investigate genome diversity in this morphospecies, we generated genome assemblies for 15 phylogenetically and geographically diverse strains of <em>P. parvum</em> including Hi-C guided, near-chromosome level assemblies for 2 strains. Comparative analysis revealed considerable DNA content variation between strains, ranging from 115 to 845 Mbp. Strains included haploids, diploids and polyploids, but not all differences in DNA content were due to variation in genome copy number. Haploid genome size between strains of different chemotypes differed by as much as 243 Mbp. Syntenic and phylogenetic analyses indicate that UTEX 2797, a common laboratory strain from Texas, is a hybrid that retains 2 phylogenetically distinct haplotypes. Investigation of gene families variably present across strains identified several functional categories associated with metabolic and genome size variation in <em>P. parvum</em> including genes for the biosynthesis of toxic metabolites and proliferation of transposable elements. Together, our results indicate that <em>P. parvum</em> is comprised of multiple cryptic species. These genomes provide a robust phylogenetic and genomic framework for investigations into the eco-physiological consequences of the intra- and inter-specific genetic variation present in <em>P. parvum</em> and demonstrate the need for similar resources for other HAB-forming morphospecies.</p>