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19,342 results for “Sequences”
Highly significant improvement of protein sequence alignments with AlphaFold2
<p>Data, figures and tables from the manuscript "Highly significant improvement of protein sequence alignments with AlphaFold2" (https://doi.org/10.1093/bioinformatics/btac625).</p> <p>The repository containing all the steps to replicate the analysis is available at GitHub (https://github.com/cbcrg/msa-af2-nf).</p> <p>*The authors Athanasios Baltzis and Leila Mansouri contributed equally.</p>
Genome sequences of Rhizopogon roseolus, Mariannaea elegans, Myrothecium verrucaria, and Sphaerostilbella broomeana and the identification of biosynthetic gene clusters for fungal peptide natural products
<p>Data to accompany the paper, detailed in manifest.txt</p>
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain).
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain).
Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing
<p>Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (<em>Salvelinus fontinalis</em>) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed non-convergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load, (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic, and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.</p>
The cDNA sequence data of hox genes in Daphnia similoides sinensis
<p><span><span><span><span><span><span><span><span><span><span><span>Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of <i><span>Microcystis aeruginosa </span></i>on Hox gene expression in the mothers and offspring of <i><span>Daphnia similoides sinensis</span></i> were investigated using a mixed diet of <i><span>M. aeruginosa</span></i> and <i><span>Scenedesmus obliquus</span></i><i> </i>in two clones. The 14 Hox genes sequence were identified in D<i><span>. similoides sinensisare </span></i>through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).</span></span></span></span></span></span></span></span></span></span></span></p>
Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
<p>Activation of plant pattern-triggered immunity (PTI) relies on the recognition of microbe-derived structures, termed patterns, through plant-encoded surface-resident pattern recognition receptors (PRRs). We show that proteobacterial translation initiation factor 1 (IF1) triggers PTI in <em>Arabidopsis thaliana</em> and related Brassicaceae species. Unlike for most other immunogenic patterns, IF1 elicitor activity cannot be assigned to a small peptide epitope, suggesting that tertiary fold features are required for IF1 receptor activation. We have deployed natural variation in IF1 sensitivity to identify <em>Arabidopsis</em> leucine-rich repeat (LRR) receptor-like protein 32 (RLP32) as IF1 receptor using a restriction site-associated DNA sequencing approach. RLP32 confers IF1 sensitivity to rlp32 mutants, IF1-insensitive <em>Arabidopsis</em> accessions and IF1-insensitive <em>Nicotiana benthamiana</em>, binds IF1 specifically and forms complexes with LRR receptor kinases SOBIR1 and BAK1 to mediate signaling. Similar to other PRRs, RLP32 confers resistance to <em>Pseudomonas syringae</em>, highlighting an unexpectedly complex array of bacterial pattern sensors within a single plant species.</p>
Sequences of Staudtia kamerunensis obtained through low coverage whole genome skimming
<p>The impact of Pleistocene climatic oscillations on the biodiversity of African tropical rain forests remains poorly understood, and the Congo Basin is particularly understudied. We aim to elucidate how Pleistocene climatic oscillations shaped lowland tropical rain forests by investigating the intraspecific diversity and evolutionary history of a widespread tree species, <em>Staudtia kamerunensis</em> Warb.</p> <p>We sequenced 88 individuals of <em>Staudtia kamerunensis</em> and 1 of <em>Staudtia pterocarpa</em> using a genome skimming approach. We used maximum likelihood and Bayesian inference to infer the plastid phylogeny. We estimated the time of speciation and differentiation, genetic diversity, and we employed a continuous phylogeographic approach to infer the dispersal history of its plastid lineages.</p> <p>We identified five plastid lineages that diverged during the Early or Middle Pleistocene and are parapatric, suggesting past population fragmentation. Four lineages are endemic to Lower Guinea, and one spans the Congo Basin. We found contrasting patterns of expansion in the two regions, with a rapid and recent range expansion of the Congolian lineage in the last 200,000 years, while the spread of the Lower Guinean lineages was substantially slower.</p> <p>The contrasting demographic histories between eastern and western lineages, associated with contrasted levels of plant species richness and rates of endemism, suggest that forest cover was more stable in Lower Guinea during the Late Pleistocene than in Congolia, where the biodiversity might have been eroded before the forest re-expanded in the Congo basin. This study illustrates how a continuous phylogeographic inference approach, mostly applied so far for inferring the spread of fast-evolving pathogens over months or years, can provide new insights to reconstruct the dispersal history of tropical tree species over thousands or millions of years.</p>
FIGURE 22 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 22. Piribelba piriformis (Mihelčič, 1964), paralectotypes (originally syntypes of author). A—solenidion φ1; B— setation of genu III (GeIII), genu and tibia IV (GeIII, TiIV); C—aggenital seta and genital setae, lateral view; D—details of selected setae (all in same scale); E—details of leg setation of another specimen, genu III and IV (GeIII, GeIV), tibia and proximal part of tarsus I (TiI, TsI); F—deutonymph in lateral view (dashed area represents crack in medium where observation is more difficult). Scale bar 100 μm.
FIGURE 29 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 29. Piribelba piriformis (Mihelčič, 1964), adult specimens from Slovakia (A–E: Dreveník, F–G: Sivec). A—dorsal view of the body; B—seta le; C—general view of the body with carried load of debris on notogaster, lateral view; D—legs I–III in lateral view, E—leg IV in lateral view; F—form "lanceata", lateral view; G—form "lanceata", detail of seta d of femur IV.
FIGURE 19 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 19. Piribelba rossica (Bulanova-Zachvatkina, 1957), nymphs from Kemerovo region, light microscope images: A, B—tritonymph, apodemes III at different focus of the microscope; C, D—tritonymph, apodemes II at different focus of the microscope; E—tritonymph, part of prodorsum with lamellar seta; F—deutonymph, genu IV; G—deutonymph, part of tibia IV. Scale bar 50 μm.
FIGURE 26 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 26. Piribelba piriformis (Mihelčič, 1964), adult. Specimen from Austria (Dörfertal): A—dorsal view; B—ventral view; C—seta le in different aspects (left: dorsal to dorsolateral view, right: dorsomedial view); D—bothridial complex. Specimen from Slovakia (Sivec), form "lanceata": E—dorsal view, F—ventral view, G—anal and genital shields; H—seta of ventral and dorsal parts of the body. Scale bars 100 μm (A, B, E, F), 50 μm (D, G, H).
FIGURE 16 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 16. Piribelba rossica (Bulanova-Zachvatkina, 1957), tritonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.
FIGURE 15 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 15. Piribelba rossica (Bulanova-Zachvatkina, 1957), deutonymph from Kemerovo region: A—leg I, right, antiaxial view; B—leg II, right, antiaxial view; C—leg III, right, antiaxial view; D—leg IV, right, antiaxial view. Scale bar 100 μm.
FIGURE 14 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 14. Piribelba rossica (Bulanova-Zachvatkina, 1957), deutonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.
FIGURE 9 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 9. Piribelba rossica (Bulanova-Zachvatkina, 1957), adult from Novosibirsk (A–E) and Tuva (F–K) regions (from Bulanova-Zachvatkina collection), light microscope images: A, F—slides from the collection with type specimen; B—epimeral III–IV and anogenital plates, ventral view; C, D, I–K—notogastral setae; E—femur, genu and tibia I, antiaxial view; G— prodorsum, part, dorsal view; H—distal part of bothridial setae. Scale bars 100 μm (B, G), 50 μm (D–C, H–K).
FIGURE 11 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 11. Piribelba rossica (Bulanova-Zachvatkina, 1957), larva from Kemerovo region: A—leg I, left, antiaxial view; B—tarsus I, left, dorsal view; C—leg II, left, antiaxial view; D—leg IV, left, antiaxial view; E—genu IV, right, dorsal view. Scale bar 100 μm.
FIGURE 28 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 28. Piribelba piriformis (Mihelčič, 1964), adult specimen from Austria (Dörfertal). A —dorsal view; B—ventral view, C—lateral view, D—rostrum and mouthparts in lateral view; E—seta le in dorsal view; F—leg IV, G—detail of femur and genu IV; H—detail of tibia III and IV; I—detail of femur and genu I; J—anterior genital setae in lateral view.
FIGURE 12 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 12. Piribelba rossica (Bulanova-Zachvatkina, 1957), protonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.
FIGURE 8 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data
FIGURE 8. Piribelba rossica (Bulanova-Zachvatkina, 1957), adult from Kemerovo region, light microscope images: A–F— notogastral setae; G–J—lamellar setae (in various specimens); H—lateral view of the body. Arrow points to distal spines. Scale bars 100 μm (H), 50 μm (A–J).
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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.