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315 results for “gene diversity”
Organisation of gene programs revealed by unsupervised analysis of diverse gene-trait associations
<p>Data used for manuscript 'Organisation of gene programs revealed by unsupervised analysis of diverse gene-trait associations'.<br> </p> <p> </p> <p> </p>
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
<p>G3PO (Gene and Protein Prediction PrOgrams) Benchmark was designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms (from human to protists). <br> </p>
Supplementary material 1 from: Scacchetti P, Pansonato-Alves J, Utsunomia R, Oliveira C, Foresti F (2011) Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences. Comparative Cytogenetics 5(3): 223-235. https://doi.org/10.3897/compcytogen.v5i3.1375
Nexus file of aligned COI and COII nucleotide sequences.
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
<p><em>Carcinus maenas</em> is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing.</p> <p>Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R).</p> <p>Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.</p>
Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift
<p>Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon <em>Procyon</em> <em>lotor</em> invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific SNP markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, i.e. – less genetically diverse invasive population from Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to a new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.</p>
Sequence diversity in MAX effectors and other genes in 120 isolates of the rice blast fungus Magnaporthe oryzae
<p>- list_of_accessions_and_assembly_statistics.xlsx: list of 120 isolate and genome assembly statistics</p> <p>- assemblies.zip: genome assemblies with repeats were not masked</p> <p>- orthogroups.txt: list of orthogroups in orthogroups.zip</p> <p>-orthogroups.zip: sequences of orthogroups, as identified using Orthofinder. Sequences were aligned using translatorX (https://doi.org/10.1093/nar/gkq291)</p> <p>- single_copy_orthologs.zip: folder which contains aligned sequences of single-copy orthologs (alignment with translatorX https://doi.org/10.1093/nar/gkq291); three types of genes were distinguished: MAX effectors, other secreted proteins, and other genes; note that to produce this dataset, the 11 orthogroups that included paralogous copies of MAX effectors were split into sets of orthologous sequences using genealogies inferred using RAXML v8, yielding a total of 94 single-copy MAX orthologs; for each split orthogroup, sets of orthologous sequences were assigned a number that was added to the orthogroup’s identifier as a suffix (for instance paralogous sequences of orthogroup OG0000244 were split into orthogroups OG0000244_1 and OG0000244_2)</p>
Supplemental data for: Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma
<p><em>Trichoderma</em> is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like <em>Trichoderma</em>, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight <em>Trichoderma</em> genomes representing the full breadth of environmental <em>Trichoderma</em>'s diverse lifestyles and nutritional modes. We generated four new <em>Trichoderma endophyticum</em> genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic <em>Trichoderma</em> genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken into consideration, no particular class of metabolic gene cluster was independently associated with the <em>Trichoderma</em> endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic <em>Trichoderma</em> genomes. Most genomic differences between <em>Trichoderma</em> lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that <em>Trichoderma</em> genomes may be particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to <em>Trichoderma</em>.</p>
Key files for: Comparative genomic analysis of Microcystis strain diversity using conserved marker genes
<p>Key data outputs to accompany the manuscript "Comparative genomic analysis of Microcystis strain diversity using conserved marker genes"</p>
Supplementary data for Contribution of reproductive developmental gene diversity to the morphological variability of panicle in African rice
<p> </p> <p>African rice, <em>Oryza glaberrima</em> Steud., is a crop closely related to Asian rice (Oryza sativa L.) and represents a valuable resource for enhancing biotic and abiotic resistance properties in rice cultivation. Despite extensive research on the genetic basis of panicle architecture in O. sativa, our understanding of the molecular genetic factors governing this essential trait in <em>O. glaberrima</em> remains limited. Furthermore, there is a significant knowledge gap regarding the intra- and inter-specific diversity of panicle development and architecture in relation to the domestication of rice species. To bridge these gaps, our study employed a comprehensive approach, including in silico analyses, candidate gene-based association analysis, genome-wide association analysis, and analysis of structural variants (SVs) present in GWAS sites. The findings of this study significantly contribute to our understanding of the molecular genetic factors underlying rice panicle development and architecture. Furthermore, they provide promising targets for future efforts to improve the panicle morphological traits of this essential crop.</p>
Asymmetric responses of abundance and diversity of N-cycling genes to altered precipitation in arid grasslands
<p>Precipitation changes exert a fundamental effect on the nitrogen (N) cycle in water-limited grasslands. Soil microbes are essential drivers of N cycle, and the rates and their stabilities of interrelated N-cycling processes are reflected by the abundance and diversity of N-cycling genes. Yet, little is known about how altered precipitation affects the genes involved in the entire N-cycling pathways.</p> <p>By combining a 6-year precipitation manipulation experiment (-30%, ambient, +30%, +50%) with metagenomic sequencing, we investigated the responses of N-cycling gene abundance and diversity to altered precipitation at two soil depths (0-10 and 30-50 cm).</p> <p>We found that increased precipitation enhanced the abundance of numerous key genes, leading to an acceleration of N turnover, but decreased the diversity of ammonium assimilation genes. Decreased precipitation did not reduce abundance or diversity of N-cycling genes. Most N-cycling genes showed generally consistent responses to altered precipitation in the topsoil (0-10 cm) and subsoil (30-50 cm), albeit with clear distinctions in both abundance and diversity by soil depth. These precipitation-specific responses and depth-dependent variabilities of functional genes were attributed to the distinct taxonomic composition of each N-cycling gene. Further, we quantified gross N transformation rates and found that they were well predicted by the abundance of most N-cycling genes (e.g., genes involved in ammonium assimilation and nitrification).</p> <p>Our study sheds new light on the soil N cycle under precipitation alterations from the perspective of individual gene abundance and diversity, and shows that future increases in precipitation could accelerate soil N turnover in arid and semi-arid lands. </p>
Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture
<p><span>Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in <em>Arabidopsis</em> found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.</span></p>
Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
<p><span>Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus <em>Clarkia</em>. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other <em>Clarkia </em>taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa – a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.</span></p>
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry
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Data from: Genetic diversity and gene flow decline with elevation in montane mayflies
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Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift
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Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
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Asymmetric responses of abundance and diversity of N-cycling genes to altered precipitation in arid grasslands
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Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
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Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.