Find research datasets worth reusing

opencc-by-4.0Jun 2020View details →

Data: An ESCRT-III polymerization sequence drives membrane deformation and fission

Raw data to "an ESCRT-III polymerization sequence drives membrane deformation and fission"

opencc-by-4.0Jun 2020View details →

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

Description of 1200bp amplicon primer sets and .bed and .tsv files for SARS-CoV-2 assembly using the ARTIC bioinformatics pipeline.

opencc-by-4.0Jun 2020View details →

Bias Away - Background sequence repositories

This repository contains all Background Sequences available for the following modules of our <a href="https://biasaway.uio.no/">BiasAway</a> web interface: <ul> <li>Mononucleotide distribution matched (subcommand g in the command-line tool).</li> <li>Mononucleotide distribution within a sliding window (subcommand c in the command-line tool).</li> </ul> For every organism, we provide background sequences with the following lengths: 100bp, 250bp, 500bp, 750bp and 1000bp. The genome assemblies used were: <ul> <li>Homo sapiens: hg38.</li> <li>Mus musculus: mm10.</li> <li>Rattus norvegicus: Rnor_6.0.</li> <li>Arabidopsis thaliana: TAIR10.</li> <li>Danio rerio: GRCz11.</li> <li>Drosophila melanogaster: dm6.</li> <li>Caenorhabditis elegans: WBcel235.</li> <li>Saccharomyces cerevisiae: R64-1-1.</li> <li>Schizosaccharomyces pombe: ASM294v2.</li> </ul> The code and necessary documentation to generate them can be found at our <a href="https://bitbucket.org/CBGR/biasaway_background_construction/src/master/">BitBucket repository</a>. The documentation for the BiasAway tool can be found at <a href="https://biasaway.readthedocs.io/en/latest/">readthedocs</a>.

opencc-by-4.0Aug 2019View details →

Automated identification of the mouse brain's spatial compartments from in situ sequencing data

Example data [1] for testing in situ sequencing graph-based decoding pipeline and decoding results for reproducing publication analyses. Image decoding pipeline and notebooks are available at: <a href="https://github.com/wahlby-lab/graph-iss">https://github.com/wahlby-lab/graph-iss</a> ------------ [1] Ke, Rongqin, et al. "In situ sequencing for RNA analysis in preserved tissue and cells." Nature methods 10.9 (2013): 857.

LDhat coalescent likelihood lookup table for 320 sequences with theta = 0.01

The LDhat `complete` tool uses the method of Fearnhead and Donnelly (2001) to calculate coalescent likelihoods (via importance sampling) for all possible two-locus haplotype configurations for a given number of sequences for a grid of recombination rate (rho) values. See the <a href="https://github.com/auton1/LDhat">LDhat documentation</a>. We considered the case of 320 sequences, for which there are 708400 configurations. Generating this table was computationally expensive (approximately 60,000 CPU hours), hence the interest in sharing it for reuse. The included sbatch job script illustrates how the computations were done (with GNU Parallel). The script could be adapted to compute a similar table on Linux clusters that use Slurm for cluster management/job scheduling.

opennotspecifiedNov 2015View details →

III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam

III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences

opennotspecifiedMay 2015View details →

standard with together) corner left bottom (analysis genetic the in included species among bold gene in shown oxidase-I are SE cytochrome and species the within at) % (divergence divergence sequence average The . pairwise) corner showing right upper (Matrix) %;. SE 4 ABLE (T error in Description of a new species of the Rhinolophus trifoliatus-group (Chiroptera: Rhinolophidae) from Southeast Asia

standard with together) corner left bottom (analysis genetic the in included species among bold gene in shown oxidase-I are SE cytochrome and species the within at) % (divergence divergence sequence average The . pairwise) corner showing right upper (Matrix) %;. SE 4 ABLE (T error

opennotspecifiedMar 2006View details →

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records

Aligned DNA sequence matrix for phylogenetic analyses in the article "Fifty years after: a taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species"

The aligned matrices are in fasta format. Genes are arranged as follows: Subgenus Huicundomantis (Huicundomantis.fas): 12S = 1–905 16S = 906–1820 RAG-1 = 1821–2463   Genus Lynchius (Lynchius.fas): 12S = 1–1028 16S = 1029–2313 RAG-1 = 2314–2925   Pristimantis orestes group (Pristimantis_orestes.fas): 12S = 1–964 16S = 965–2041 RAG-1 = 2042–2683

opencc-zeroJun 2020View details →

Data from: Transcriptome sequencing reveals signatures of positive selection in the spot-tailed earless lizard

The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.

Multiple alignment of DNA-B sequences from EACMV, EACMKV, EACMMV, EACMZV, SACMV (5 "species")

All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson). These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21

Multiple alignment of ICMV and SLCMV DNA-B sequences

All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl and AliView. Note added 2020-09-07: AJ575821 is listed in the file as ICMV based on its assignment in the NCBI Taxonomy database (taxa 341701 and 31600) but it is better classified as SLCMV. These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21

opencc-by-4.0Aug 2020View details →

Recombination detection program (RDP4) results for EACMV-like DNA-B sequences (7 "species")

A DNA-B multiple alignment (Zenodo record 3965023) was scanned with RDP4.97 (D. Martin et al. 2015). The input sequences belong to 7 “species”: CMMGV, EACMCV, EACMV, EACMKV, EACMMV, EACMZV, SACMV. Recombination breakpoints for events with statistical support from at least 5 of 7 methods were adjusted per the manual. These events were explicitly accepted, with the exception of one event which lost significance after adjustment of breakpoints. A CSV file with the results was exported and then saved a second time with Excel to normalize format (a comma in between every column). These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21

Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples

Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.

opencc-zeroDec 2019View details →

Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status

Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (Crotalus oreganus) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.

Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the four species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all four species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

Didimosphenia geminata: sequences and morphology data set

Microalgae and their invasiveness are recurrent themes in aquatic environments and many invasions by microalgae are linked to eutrophication. However the diatom Didymosphenia geminata has gained notoriety in forming thick mucilaginous mats in pristine, rocky-bottomed rivers with no obvious connection to elevated levels of nutrients. This species is native to freshwaters of the circumboreal region of the Northern Hemisphere and blooms in the Southern Hemisphere have been attributed to recent introductions of the species to these regions. Although regional population genetic analyses have suggested multiple recent introduction of this species, the gene flow and the spatial genetic diversity distribution on a global scale remains unknown. We develop a phylogeographic analysis to investigate the genetic diversity of D. geminata populations around the globe. Our results indicate two distinct genetic lineages geographically distributed that remain spatially isolated. One lineage is exclusively found in Europe, the other is distributed in North America, New Zealand and South America. Since blooms of D. geminata commenced in North America and in Europe simultaneously, these data support the idea that factors associated with global environmental change and possibly the associated biome are the cause of blooms globally. We further discuss the role of human mediated-dispersal.

Phylogeny estimation given sequence length heterogeneity

Abstract Phylogeny estimation is a major step in many biological studies, and has many well known challenges. With the dropping cost of sequencing technologies, biologists now have increasingly large datasets available for use in phylogeny estimation. Here we address the challenge of estimating a tree given large datasets with a combination of full-length sequences and fragmentary sequences, which can arise due to a variety of reasons, including sample collection, sequencing technologies, and analytical pipelines. We compare two basic approaches: (1) computing an alignment on the full dataset and then computing a maximum likelihood tree on the alignment, or (2) constructing an alignment and tree on the full length sequences and then using phylogenetic placement to add the remaining sequences (which will generally be fragmentary) into the tree. We explore these two approaches on a range of simulated datasets, each with 1000 sequences and varying in rates of evolution, and two biological datasets. Our study shows some striking performance differences between methods, especially when there is substantial sequence length heterogeneity and high rates of evolution. We find in particular that using UPP to align sequences and RAxML to compute a tree on the alignment provides the best accuracy, substantially outperforming trees computed using phylogenetic placement methods. We also find that FastTree has poor accuracy on alignments containing fragmentary sequences. Overall, our study provides insights into the literature comparing different methods and pipelines for phylogenetic estimation, and suggests directions for future method development.

Sequences of Pitcairnia flammea

Geographic isolation and reduced population sizes can lead to local extinction, low efficacy of selection, and decreased speciation. However, population differentiation is an essential step of biological diversification. In allopatric speciation, geographically isolated populations differentiate and persist until the evolution of reproductive isolation and ecological divergence complete the speciation process. Pitcairnia flammea allow us to study the evolutionary consequences of habitat fragmentation on naturally disjoint rock outcrop species from the Brazilian Atlantic Rainforest (BAF). Our main results showed low to moderate genetic diversity within populations, and deep population structuring caused by limited gene flow, low connectivity, genetic drift and inbreeding of long-term isolation and persistence of rock outcrops populations throughout Quaternary climatic oscillations. Bayesian phylogenetic and model-based clustering analyses found no clear northern and southern phylogeographic structure commonly reported for many BAF organisms. Although, we found two main lineages diverging by approximately 2 Mya during the early Pleistocene, species delimitation analysis assigned most of the populations as independent evolving entities, suggesting an important role of disjoint rock outcrops in promoting high endemism in this rich biome. Lastly, we detected limited gene flow in sympatric populations although some hybridization and introgression were observed, suggesting a continuous of speciation processes in this species complex. Our data not only inform us about the extensive differentiation and limited gene flow found among Pitcairnia flammea species complex, they also contain information about the mechanisms that shape the genetic architecture of small and fragmented populations of isolated rock outcrop of recently radiated plants.

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon's diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.