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46 results for “insect genome”
GC-MS data set for Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>RAW GC/MS data set for characterization of class II terpene synthases from <em>Callicarpa americana </em></p>
Data from: Regulatory genome annotation for 33 insect species
<p>Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation of insect regulatory sequences, and provide a searchable database resource with enhancer predictions for 33 genomes. Using our previously-developed SCRMshaw computational enhancer prediction method, we predict over 2.8 million regulatory sequences along with the tissues where they are expected to be active, in a set of insect species ranging over 360 million years of evolution. Extensive analysis and validation of the data provides several lines of evidence suggesting that we achieve a high true-positive rate for enhancer prediction. One, we show that our predictions target specific loci, rather than random genomic locations. Two, we predict enhancers in orthologous loci across a diverged set of species to a significantly higher degree than random expectation would allow. Three, we demonstrate that our predictions are highly enriched for regions of accessible chromatin. Four, we achieve a validation rate in excess of 70% using in vivo reporter gene assays. As we continue to annotate both new tissues and new species, our regulatory annotation resource will provide a rich source of data for the research community and will have utility for both small-scale (single gene, single species) and large-scale (many genes, many species) studies of gene regulation. In particular, the ability to search for functionally-related regulatory elements in orthologous loci should greatly facilitate studies of enhancer evolution even among distantly related species.</p>
Supplementary Files and Data of 'Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond'
<p> Live birth (viviparity) has arisen repeatedly and independently among animals. We sequenced the genome and transcriptome of the viviparous Pacific beetle-mimic cockroach and performed comparative analyses with two other viviparous insect lineages, tsetse flies and aphids, to unravel the basis underlying the transition to viviparity in insects. We identified pathways undergoing adaptive evolution for insects, involved in uro-genital remodeling, tracheal system, heart development, and nutrient metabolism. Transcriptomic analysis in the cockroach and tsetse viviparity reveals that uterine remodeling and nutrient production are increased and the immune response is altered during pregnancy, facilitating structural and physiological changes to accommodate and nourish the progeny. These patterns of convergent evolution of viviparity among insects, together with similar adaptive mechanisms identified among vertebrates, highlight that the transition to viviparity requires changes in uro-genital remodeling, enhanced tracheal and heart development (corresponding to angiogenesis in vertebrates), nutrient metabolism, and shifted immunity in all animal systems.</p>
Data from: Regulatory genome annotation for 33 insect species
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Data from: Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion
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First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
<p>Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. </p>
A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects
<p><em>Neoneuromus ignobilis</em> is an archaic holometabolous aquatic predatory insect. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for adaptive evolution. Here, we provided a high-contiguity, chromosome-level genome assembly of <em>N</em>. <em>ignobilis</em> using high coverage nanopore reads and the Hi-C technique. The final assembly is 481.43 MB in size, containing 12 telomere-ended pseudochromosomes with only 23 gaps. We then compared 42 hexapod species genomes including six independent lineages comprising 11 aquatic insects, and found convergent expansions of long wavelength-sensitive and blue-sensitive opsins, thermal stress response TRP channels, and sulfotransferases in aquatic insects, which may be related to their aquatic adaptation. We also detected strong non-random signals of convergent amino acid substitutions in aquatic insects. Collectively, our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitutions.</p>
Data from: Transitions between phases of genomic differentiation during stick-insect speciation
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.
Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects
<p>Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar, because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental, and phenotypic data with Bayesian modeling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of <em>Timema</em> stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (i.e., habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits, and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.</p>
Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects
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First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
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Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
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A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects
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Data from: Transitions between phases of genomic differentiation during stick-insect speciation
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Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>Background: Plants exhibit wide chemical diversity due to production of specialized metabolites which function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs and as sources of insect repellents, health-promoting compounds, and fragrance. Findings: We report the chromosome-scale genome assembly of <em>Callicarpa americana</em> L. (American beautyberry), a species within the early diverging Callicarpoideae clade of the Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long reads and Hi-C scaffolding, we generated a 506.1 Mb assembly spanning 17 pseudomolecules with an N50 contig and N50 scaffold size of 7.5 Mb and 29.0 Mb, respectively. A total of 32,164 genes was annotated including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Whole genome duplication analyses revealed three putative events, which together with local tandem duplication events, contributed to gene family expa, American beautyberransion of terpene synthases. Kolavenyl diphosphate is a gateway to many of <em>C. americana</em>'s bioactive terpenoids; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with <em>Tectona grandis</em> L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 <em>C. americana</em> syntelogs. Conclusions: Access to the <em>C. americana</em> genome provides a roadmap for rapid discovery of genes encoding plant-derived agrichemicals and a key resource to understand the evolution of chemical diversity in Lamiaceae. </p> <p> </p>
The genome sequence of Samia ricini, a new model species of lepidopteran insect
<p><span><span><span><span><span><span><span><span><span><span><span><i>Samia ricini</i>, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Since <i>S. ricini </i>is much more tough and resistant to diseases than the current model species <i>Bombyx mori</i>, the former can be easily reared compared to the latter. In addition, genetic resources available for <i>S. ricini</i> rival or even exceed those for <i>B. mori</i>: at least 26 eco-races of <i>S. ricini</i> are reported and <i>S. ricini</i> can hybridize with wild <i>Samia</i> species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour, larval spot pattern, etc. are different between<i> S. ricini</i>and wild <i>Samia</i> species so that those traits can be the target for forward genetic analysis.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span> In order to facilitate genetic research in <i>S. ricini</i>, we determined the whole genome sequence of <i>S. ricini</i>. The assembled genome of <i>S. ricini</i> was 458 Mb with 155 scaffolds, and the N50 length of the assembly was approximately 21 Mb. 16,702 protein coding genes were predicted in the assembly. Although the gene repertoire of <i>S. ricini</i> was not so different from that of <i>B. mori</i>, some genes, such as chorion genes and fibroin genes, seemed to have specifically evolved in <i>S. ricin</i></span></span></span></span></span></span></span></span></span></span></span><em>i</em>.</p>
Genomics reveals widespread ecological speciation in flightless insects
<p><span>Recent genomic analyses have highlighted parallel divergence in response to ecological gradients, but the extent to which altitude can underpin such repeated speciation remains unclear.</span> Wing reduction and flight loss have apparently evolved repeatedly in montane insect assemblages, and have been suggested as important drivers of hexapod diversification. We test this hypothesis using genomic analyses of a widespread wing-polymorphic stonefly species complex in New Zealand. We identified over 50,000 polymorphic genetic markers generated across almost 200 <i>Zelandoperla fenestrata</i> stonefly specimens using a newly generated plecopteran reference genome, to reveal widespread parallel speciation between sympatric full-winged and wing-reduced ecotypes. <span>Rather than the existence of a single, widespread, flightless taxon (<i>Zelandoperla pennulata</i>), evolutionary genomic data reveal that wing-reduced upland lineages have speciated repeatedly and independently from full-winged <i>Z. fenestrata</i>.</span> This repeated evolution of reproductive isolation between local ecotype pairs that lack mitochondrial DNA differentiation suggests that ecological speciation has evolved recently. A cluster of outlier SNPs detected in independently wing-reduced lineages, tightly linked in an approximately 85 kb genomic region that includes the developmental 'supergene' <i>doublesex</i>, suggests that this 'island of divergence' may play a key role in rapid ecological speciation.</p>
Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
Fig. 3 in Genomics Reveals Exceptional Phylogenetic Diversity Within a Narrow-Range Flightless Insect
Fig. 3. Phylogenetic reconstruction reveals three well-supported Zelandoperla maungatuaensis clades. (a) Bayesian maximum likelihood consensus phylogeny illustrating the relationships among Z. maungatuaensis lineages based on the mitochondrial COI gene. Posterior probability values are noted above each node. Outgroups (Zelandoperla agnetis and Zelandoperla denticulata) are excluded for diagrammatic clarity. (b) Midpoint rooted maximum likelihood phylogeny illustrating genome-wide relationships among Z. maungatuaensis lineages, based on 10,429 SNP markers. IQTREE ultrafast bootstrap values ≥ 90 are indicated at each node.
Fig. 2 in Genomics Reveals Exceptional Phylogenetic Diversity Within a Narrow-Range Flightless Insect
Fig. 2. Striking genetic substructuring across the narrow geographic range of Zelandoperla maungatuaensis. (a) Collection localities (coloured circles) for Z. maungatuaensis across the Maungatua range.White crosses indicate sites where Z. maungatuaensis has not been found. (b) Principal component analysis, based on 10,429 genome-wide SNPs, illustrating the genetic differentiation among Northern, Southern, and Central Z. maungatuaensis lineages.
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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.