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2,848 results for “sequence data”
Data from: ITS all right mama: Investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: Perseus and UCHIME. Large proportions of the chimeras reported were false positives. No false negatives were found in the dataset. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric "parent sequences" had significantly higher percent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighboring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seem to buffer the rate of chimera formation in comparison to other, less variable barcoding regions, due to shorter regions of high sequence similarity.
Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently—within the last two million years—and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.
Data from: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.
Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data
Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.
Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences
<p>Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences</p>
MS coverage HTT sequence and assessment of the data so far (2016/02/23)
<p>Open lab notebook for project: huntingtin structural studies</p> <p> </p>
FIGURES 510. Lamyctes hellyeri n in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 510. Lamyctes hellyeri n. sp. 5, 10, QVMAG 23:23044, holotype female. 5, dorsal habitus, scale 1 mm; 10, ventral view of posterior segments and gonopods, scale 100 m. 69, QVMAG 23:23045, female, scale 0.5 mm. 6, leg 12; 7, leg 13; 8, leg 14; 9, leg 15.
FIGURES 2633. Lamyctes hellyeri n in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 2633. Lamyctes hellyeri n. sp. 2631, QVMAG 23:23046, female. 2627, gnathal edge of mandible and detail of ventral part, scales 10 m; 28, aciculae, scale 10 m; 29, 30, fringe of branching bristles, on successively more dorsal part of mandible, scales 10 m; 31, sternite of segment 15 and posterior margin of sternite 14, scale 100 m. 3233, QVMAG 23:23047, female, gonopod and detail of spurs and claw, scales 50 m, 10 m.
FIGURE 38 in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURE 38. Cladograms based on molecular sequence data. Cladograms at left are shortest based on parameter set (121) that minimises incongruence between genes; cladograms at right are strict consensus of all 15 explored parameter sets. Numbers at nodes are parsimony jackknife frequencies. From left to right, top to bottom: cladograms based on combined molecular data (2198 steps); cladograms based on 18S rRNA (562 steps); cladograms based on 28S rRNA (98 steps); cladograms based on 16S rRNA (616 steps); cladograms based on COI (901 steps).
FIGURES 3437. Lamyctes hellyeri n in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 3437. Lamyctes hellyeri n. sp. QVMAG 23:23048, female, pretarsus of leg 14, scales 10 m. 3436, anterior, posterior, and ventral views; 37, detail of lateral pore and ornament on scutes of main claw.
FIGURES 1825. Lamyctes hellyeri n in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 1825. Lamyctes hellyeri n. sp. QVMAG 23:23046, female. 18, ventral view of maxillipede, scale 100 m; 1920, dental margin of maxillipede coxosternite, scales 50 m, 10 m; 21, tarsus and claw of second maxilla, scale 50 m; 22, distal part of tarsus and claw of second maxilla, scale 10 m; 23, coxal projections and telopods of first maxillae, scale 50 m; 24, first maxillae, scale 100 m; 25, plumose setae on inner margins of telopods of first maxillae, scale 10 m.
FIGURES 1117. Lamyctes hellyeri n in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 1117. Lamyctes hellyeri n. sp. 11, 1417, QVMAG 23:23046, female. 11, anterior part of head shield and basal part of antennae, scale 100 m; 14, sensilla on dorsal side of antenna, scale 10 m; 1516, antennal articles, dorsal side, scales 50 m; 17, cephalic pleurite with Tömösváry organ, scale 50 m. 1213, QVMAG 23:23047, female. 12, ventral view of clypeus and labrum, scale 100 m; 13, labral midpiece and inner parts of sidepieces, scale 30 m.
FIGURES 14 in A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes Henicops Group
FIGURES 14. Lamyctes coeculus (Brölemann). 1, 3, AM KS57961, female, Mellong Range, NSW, Australia. 2, 4, MCZ DNA100472, female, Cerro San Javier, Tucumán, Argentina. 12, ventral view of head, scales 100 m; 34, dental margin of maxillipede coxosternite, scales 50 m.
FIGURE 4. A-M in A new genus of Lysitermini (Hymenoptera: Braconidae: Lysiterminae) from Madagascar and its taxonomic placement based on 28 S rDNA sequence data
FIGURE 4. A-M. Morphological features of Lysitermini. Metasoma (A, C, D, G, H, dorsal view; B, E, F, lateral view), areolation of propodeum (J), mesoscutum (I, K), and third metasomal tergum (L, M). A, B. Afrotritermus capensis (Hedqvist). C. Neolysitermus turneri Belokobylskij & Quicke. D, E. Acanthormius japonicus Ashmead. F, J. Lysitermus pallidus Foerster. G. Aulosaphanes suturalis (Belokobylskij). H, L. Aulosaphes psychidivorus Muesebeck. K. Austrolysitermus hirsutus Belokobylskij. I, M. Aulosaphoides lampas (Nixon).
FIGURE 3. A–I in A new genus of Lysitermini (Hymenoptera: Braconidae: Lysiterminae) from Madagascar and its taxonomic placement based on 28 S rDNA sequence data
FIGURE 3. A–I. Fore and hind wings of Lysitermini. A. Tritermus tobiasi van Achterberg. B. Afrotritermus brachypterus Belokobylskij. C. Afrotritermus capensis (Hedqvist). D. Austrolysitermus hirsutus Belokobylskij. E. Lysitermus pallidus Foerster. F. Acanthormius japonicus Ashmead. G. Aulosaphanes suturalis (Belokobylskij). H. Aulosaphoides lampas (Nixon). I. Aulosaphes psychidivorus Muesebeck.
FIGURE 2 in A new genus of Lysitermini (Hymenoptera: Braconidae: Lysiterminae) from Madagascar and its taxonomic placement based on 28 S rDNA sequence data
FIGURE 2. Morphological features of Atritermus pedestris gen. & sp. n. A. Mesosoma, lateral view. B. Head and base of mandible, lateral view.
FIGURE 1 in A new genus of Lysitermini (Hymenoptera: Braconidae: Lysiterminae) from Madagascar and its taxonomic placement based on 28 S rDNA sequence data
FIGURE 1. Morphological features of Atritermus pedestris gen. & sp. n. A. Habitus, lateral view. B. Metasoma, dorsal view.
FIGURE 5 in A new genus of Lysitermini (Hymenoptera: Braconidae: Lysiterminae) from Madagascar and its taxonomic placement based on 28 S rDNA sequence data
FIGURE 5. Majority rule phylogram resulting from consensus of postburn-in trees recovered in the two Bayesian analyses of the 28S data set. Black circles above branches indicate clades with posterior probabilities? 0.95.
FIGURES 1–9. 1–3. Philophylla millei, n in A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data
FIGURES 1–9. 1–3. Philophylla millei, n. sp., holotype male. 4. P. millei, n. sp., paratype female. 5. Anastrephoides matsumurai Shiraki, female. 6. Myoleja korneyevi Han & Kütük, female. 7. M. korneyevi, male. 8. Anastrepha barnesi Aldrich. 9. Anastrepha obliqua (Macquart). Abbreviations: AAB = anterior apical band; PAB = posterior apical band; RMB = radial-medial band; SAB = subapical band; SCB = subcostal band.
FIGURE 16 in A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data
FIGURE 16. Relationships of the tribe Trypetini inferred from neighbor-joining tree based on Kimura two parameter distances (1159 bp after gaps and sites with missing data removed). The first number is the Pc value from the standard error test (higher than 90%), and the second number is the Pb from the bootstrap test (2000 replications).
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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.