Hamlet genome and speciation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27858 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| UXGA01.dat.gz | Other | |||
| UXGA01.fasta.gz | Fasta.gz | |||
| UXGA01.master.dat | Other | |||
| ERR2750990_1.fastq.gz | Fastqsanger.gz |
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Project description:We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.
2019-02-05 | GSE105080 | GEO
Project description:We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.
2019-02-05 | GSE111022 | GEO
Project description:We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.
2019-02-05 | GSE109889 | GEO
Project description:Contrasting signatures of genomic divergence during sympatric speciation
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Project description:Background: The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts have small genomes, can be easily cultured, and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair has been found, between S. bayanus and S. cerevisiae, comprising the mitochondrially targeted product of a nuclear gene, AEP2, and a mitochondrially encoded locus, OLI1, the 5' region of whose transcript is bound by Aep2. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. Methods: We report here the first detailed genome-wide analysis of rare F2 progeny from an otherwise sterile hybrid, and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions may be responsible for their post-zygotic separation. These interactions most likely involve multiple loci having weak effects, as there were multiple significant pairwise combinations of loci, with no single combination being completely excluded from the viable F2s. Conclusions: The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions, suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that "death by a thousand cuts" leads to speciation, whereby an accumulation of polymorphisms can lead to an incompatibility between the species "transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. Genotypes for hybrids between S. cerevisiae and S. paradoxus. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
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Project description:<p>The section <em>Oleifera</em> (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. <em>Oleifera</em> using diploid wild <em>Camellia lanceoleosa</em> with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. <em>Camellia lanceoleosa</em> underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of <em>C</em>. <em>lanceoleosa</em> and <em>Camellia sinensis</em> (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in <em>C</em>. <em>lanceoleosa</em> were significantly enriched in oil biosynthesis, and the expansion of homomeric <em>acetyl-coenzyme A carboxylase</em> (<em>ACCase</em>) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3-phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in <em>C. lanceoleosa</em>. Theanine and catechins were present in the leaves of <em>C</em>. <em>lanceoleosa</em>. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent <em>N</em>-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of <em>C. lanceoleosa</em> is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. <em>Oleifera</em>.</p>
2022-07-14 | MTBLS3769 | MetaboLights
Project description:It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. However, the manner in which epigenetic changes are generated remains unknown. Although whole-genome DNA methylation profiles in some somatic tissues and sperm have been reported for humans and chimpanzees, a systematic analysis of these data has been lacking. In this manuscript, therefore, we analyzed these methylomes in detail, identified genomic regions with different DNA methylation levels, and examined the cell-type specificity and its association with changes in genomic sequence. Moreover, we generated a methylation map of Japanese macaque sperm and used it as an out-group to infer the evolutional history of methylation in these regions.
2017-01-22 | GSE64829 | GEO
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>
2023-04-26 | MTBLS5893 | MetaboLights
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