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2,848 results for “sequence data”
Data from: Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing
Recent genomic studies show that introgression can occur at a genome-wide scale among recently diverged lineages. However, introgression is difficult to distinguish from incomplete lineage sorting (ILS), and these processes are expected to occur together. Moreover, ncDNA introgression is less easily detected than mtDNA introgression, and as such its prevalence is less well understood. The Chinese horseshoe bat (Rhinolophus sinicus) occurs as three distinct forms on mainland China: the subspecies R. s. septentrionalis and two parapatric clades of R. s. sinicus (Central and East R. s. sinicus). Previous work suggested widespread mtDNA introgression between these subspecies; however, no ncDNA introgression was detected. In this study we sampled the coding genomes of all three forms of R. sinicus in order to perform a more sensitive test for ncDNA introgression against an expected background of ILS. We assembled 3548 nuclear protein-coding genes from these and three congeneric species, and built a high-confidence species tree using maximum likelihood and Bayesian concordance methods. Phylogenetic analysis suggested a mosaic genome for Central R. s. sinicus derived from R. s. septentrionalis and East R. s. sinicus. Nuclear DNA introgression between Central R. s. sinicus and R. s. septentrionalis was supported by three different tests, whereas ILS could not be ruled out completely. Our findings, in line with other recent results, indicate that recently diverged taxa undergo large-scale secondary introgression, and that this process likely operates alongside ILS to give rise to phylogenomic discordances or even mosaic genomes.
Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
Data from: Multiplex PCR targeting lineage specific SNPs ‐ A highly efficient and simple approach to block out predator sequences in molecular gut content analysis
Background: Food webs form the basis of biological communities, though empirical research has been hindered by difficulties in quantifying interactions. Metabarcoding from predator gut content extractions with universal primers promises to provide simple and rapid insights into food web interactions. However, the highly overabundant predator DNA often completely outcompetes that of the digested prey DNA during PCR, impeding the ability to assess the abundance and diversity of prey items. Methods: Focusing on the issue of overabundance of predator DNA amplified by a commonly used COI primer pair, we use predator lineage-specific SNPs at the 3'-end of PCR primers to selectively block out predators from amplification. While this approach largely prevents predator amplification, it retains high taxonomic versatility for prey lineages. We introduce a novel multilocus assay, targeting four nuclear and mitochondrial rDNA markers and test our approach in a diverse set of spiders from 12 families. We estimate the recovered prey DNA proportions and compare the taxonomic composition of prey communities between markers. Using a feeding experiment, we also explore recovery of prey DNA over time. Results: While commonly used COI primers yield low and very unpredictable amounts of prey DNA, our assay allows for a considerable and consistent prey enrichment across all tested species. The recovered prey's taxonomic composition is comparable between markers and supports results acquired by COI. The new marker set can be amplified in a simple multiplex PCR, considerably reducing the necessary workload. Conclusions: Our multi-locus approach allows the generation of an unprecedented amount of prey data at low cost and effort. Lineage specific PCR is taxonomically versatile and could readily be adapted to any prey-predator interaction, opening up the opportunity for community-wide studies on food web interactions.
Data from: Haplotype-phased synthetic long reads from short-read sequencing
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIV env gene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.
Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation - Supplementary Data
<p>Genotype data for 19 cell lines from the Yoruba HapMap population that were used in this study, and summary statistics from QTL calling (see README.md in summary.zip).</p>
Data from: High-throughput sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma
[No abstract entered]
Data from: Phylogenetic Systematics and Evolution of Primate-Derived Pneumocystis Based on Mitochondrial or Nuclear DNA Sequence Comparison
[No abstract entered]
Figure 1 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655
Figure 1 - The sampling locality of Kibaleana apicospinosa sp. n. in southern Uganda.
Figure 2 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655
Figure 2 - Malaise trapping at Kibale National Park in southern Uganda (Photo by O. Kurina).
Statistical data for "Recent advances and perspectives on whole genome sequencing of insects: A review"
<p>This is the statistical data for "Recent advances and perspectives on whole genome sequencing of insects: A review", and derived from NCBI-Genome database. </p>
18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p>Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) were pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation; the procedure was implemented in a custom bash script. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (<span><span><a href="https://benjjneb.github.io/dada2/tutorial.html" target="_blank" rel="noopener">https://benjjneb.github.io/dada2/tutorial.html</a></span></span>); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN = 0 of function filterAndTrim). Filtered forward (F) and reverse (R) reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; allowing no mismatches in read merging (default parameter maxMismatch = 0 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1,293 sequences from GoN protist strains and fungi environmental sequences. Highest bit score matching with the best taxonomic resolution were then selected among the returned results.</p>
Fig. 4 in Towards resolving the double classification in Erythraeus (Actinotrichida: Erythraeidae): matching larvae with adults using 28S sequence data and experimental rearing
Fig. 4 Erythraeus phalangoides, larva. Habitus
Fig. 15 in Towards resolving the double classification in Erythraeus (Actinotrichida: Erythraeidae): matching larvae with adults using 28S sequence data and experimental rearing
Fig. 15 Erythraeus regalis, larva. Scutum
Figure 7 from: Ji X-H, Vlasák J, Tian X-M, Dai Y-C (2018) Three new species of Fomitiporella (Hymenochaetales, Basidiomycota) based on the evidence from morphology and DNA sequence data. MycoKeys 30: 73-89. https://doi.org/10.3897/mycokeys.30.23109
Figure 7 Basidiomata of Fomitiporella vietnamensis. Scale bar: 1 cm.
Figure 3 from: Ji X-H, Vlasák J, Tian X-M, Dai Y-C (2018) Three new species of Fomitiporella (Hymenochaetales, Basidiomycota) based on the evidence from morphology and DNA sequence data. MycoKeys 30: 73-89. https://doi.org/10.3897/mycokeys.30.23109
Figure 3 A basidiocarp of Fomitiporella austroasiana. Scale bar: 1 cm.
Figure 5 from: Ji X-H, Vlasák J, Tian X-M, Dai Y-C (2018) Three new species of Fomitiporella (Hymenochaetales, Basidiomycota) based on the evidence from morphology and DNA sequence data. MycoKeys 30: 73-89. https://doi.org/10.3897/mycokeys.30.23109
Figure 5 Basidiomata of Fomitiporella mangrovei. Scale bar: 5 cm.
Figure 1 from: Tibpromma S, Hyde K, Bhat J, Mortimer P, Xu J, Promputtha I, Doilom M, Yang J, Tang A, Karunarathna S (2018) Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 33: 25-67. https://doi.org/10.3897/mycokeys.33.23670
Figure 1 Habitats of the host plants: a, b Pandanus spp. c, d Freycinetia spp.
Figure 1 from: Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. https://doi.org/10.3897/mycokeys.39.28109
Figure 1 - Outline of workflow in different analysis pipelines.
Figure 1 from: Tibpromma S, Hyde K, Bhat J, Mortimer P, Xu J, Promputtha I, Doilom M, Yang J, Tang A, Karunarathna S (2018) Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 33: 25-67. https://doi.org/10.3897/mycokeys.33.23670
Figure 1 - Habitats of the host plants: a, b Pandanus spp. c, d Freycinetia spp.
Score matching for differential abundance testing of compositional high-throughput sequencing data - data repository
<p>Data repository for "Score matching for differential abundance testing<br>of compositional high-throughput sequencing data" (<a href="https://github.com/bio-datascience/cosmoDA">github</a>)</p> <p>To use, clone the repository, then download the zip file and unpack it in the main directory of the repository.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.