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Dataset results
12 results for “de novo evolution”
Something old, something new: evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization
<p>Weedy rice (<i>Oryza</i> spp.) is a worldwide weed of domesticated rice (<i>O. sativa</i>), considered particularly problematic due to its strong competition with the crop, which leads to reduction of yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the U.S. and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild<i> Oryza </i>species, local cultivated varieties, and exotic <i>Oryza</i> groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild <i>Oryza </i>species<i> </i>(<i>O. glumaepatula</i>, <i>O. grandiglumis</i>, <i>O. latifolia </i>and <i>O. alta</i>) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local <i>indica</i> cultivars, and has also likely been inadvertently imported as an exotic pest from the US. Additionally, weeds comprising <i>de novo</i> admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.</p>
Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
<p>Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene-concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.</p>
Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
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Something old, something new: evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization
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Data from: Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences
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Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles
Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as "horns". These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce a horn at all, or they produce a disproportionately small horn for their body size. While the diversity of horn shapes and their behavioural ecology have been reasonably well studied, we know far less about the proximate mechanisms that regulate horn growth. Thus, using 454 pyrosequencing, we generated transcriptome profiles, during horn growth and development, in two different scarab beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and the dung beetle, Onthophagus nigriventris. We obtained over half a million reads for each species that were assembled into over 6,000 and 16,000 contigs respectively. We combined these data with previously published studies to look for signatures of molecular evolution. We found a small subset of genes with horn-biased expression showing evidence for recent positive selection, as is expected with sexual selection on horn size. We also found evidence of relaxed selection present in genes that demonstrated biased expression between horned and horn-less morphs, consistent with the theory of developmental decoupling of phenotypically plastic traits.
Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles
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De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A-rearranged leukemia
GEO Series GSE106714. Mus musculus. 45 samples. Type: Expression profiling by high throughput sequencing.
Evaluation of Sirolimus-Eluting, Heparin-Coated CoCr Stent in the Treatment of de Novo Coronary Artery Lesions in Small Vessels(EVOLUTION)
ClinicalTrials.gov study NCT00233779. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes
GEO Series GSE35563. Silene latifolia. 6 samples. Type: Expression profiling by high throughput sequencing.
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
GEO Series GSE173861. Saccharomyces cerevisiae. 2 samples. Type: Expression profiling by high throughput sequencing.
Run or die in the evolution of de novo microRNAs
GEO Series GSE110086. Drosophila sechellia; Drosophila simulans; Drosophila melanogaster; Drosophila erecta. 10 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.