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opencc-by-4.0Mar 2022View details →

Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)

Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper. PacBio.simulated_uniform_coverage.fasta.gz and ONT.simulated_uniform_coverage.fasta.gz files were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”. ONT.simulated_real_expression.fasta.gz file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". mouse.gencode.M26.spatial.15percent.reduced.gtf was used as the annotation file for all tools. mouse.gencode.M26.spatial.15percent.expressed.gtf contains the set of all expressed isoforms. mouse.gencode.M26.spatial.15percent.expressed_kept.gtf contains those of the isoforms that are in presented in the annotation file ("known" transcripts), mouse.gencode.M26.spatial.15percent.reduced.gtf contains expressed isoforms that were removed from the annotation ("novel" transcripts).

opencc-by-4.0Mar 2022View details →

Importance of hematite self-reversal in Al-rich soils magnetostratigraphy: Revisiting the Damei red soil sequence in the Bose Basin, southern China

This is the data of the article titled "Importance of hematite self-reversal in Al-rich soils magnetostratigraphy: Revisiting the Damei red soil sequence in the Bose Basin, southern China" which submitted for publication to JGR-Solid Earth under the reference # 2021JB023165

opencc-zeroMar 2022View details →

Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

Processed MinION genome sequencing data for strains ILHA G3AG5 and ILHA G3AA5

Strain G3AA5 datasets include: Galaxy2750, Galaxy2754, Galaxy3522, Galaxy3523, Galaxy3524, Galaxy3541   Strain G3AG4 datasets include: Galaxy2404, Galaxy2408, Galaxy3517, Galaxy3518, Galaxy3519, Galaxy3539

opencc-by-4.0Dec 2021View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "Dos nuevas especies del grupo Pristimantis boulengeri (Anura: Strabomantidae) de la cuenca alta del río Napo, Ecuador" by Bejarano, et al.

Matrix in nexus format that include sequences of 16S (1-1295), RAG1 (1296-1922), 12S (1923-3306), and COI (3307-3984) for 97 specimens belonging to the genus Pristimantis, in addition to specimens of Strabomantis and Niceforonia as outgroups.

Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma

Premise Genera that are widespread but have a geographically discontinuous distribution and are represented by few species are intriguing. Did they achieve their disjunct distribution recently, or is it ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale floristic pattern in which closely related species appear co-distributed in isolated regions over the edges of Africa and nearby archipelagos. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other at the ends of the African continent: C. canariense in the west, endemic to the Canary Islands; C. lyperiiflorum in the east, endemic to the Horn of Africa - Southern Arabia; and C. rotundifolia, restricted to Southern Africa. Methods Here, we employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae, using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian MCMC approaches. Population history was estimated with phylogeographic structured coalescent methods. Key Results Our results support C. rotundifolia as sister to the disjunct clade formed by C. canariense and C. lyperiiflorum. Stem divergence was dated in the Late Miocene, while the origin of extant diversification within the genus was inferred as Early Pliocene. Conclusions We show that the current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, consistent with the "climatic refugia" hypothesis.

Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency

Alzheimer's disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD we found that cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it one of the earlier defects in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. To delineate potential self-renewal pathways that might contribute to the defect and rescue of Tg-SwDI NPCs and Tg-SwDI/Usp16+/- NPCs, respectively, we performed single-cell RNA-seq and gene set enrichment analysis (GSEA) on lineage depleted primary FACS-sorted CD31-CD45-Ter119-CD24- NPCs from Tg-SwDI, WT, and Tg-SwDI/Usp16+/- mice at 3-4 months and 1 year of age. Using the GSEA Hallmark gene sets, we found only three gene sets that were enriched in Tg-SwDI mice over WT mice and rescued in the Tg-SwDI/Usp16+/- mice at both ages: TGF-ß pathway, oxidative phosphorylation, and Myc Targets. The TGF-ß pathway consistently had the highest normalized enrichment score in pairwise comparisons between Tg-SwDI vs WT and Tg-SwDI vs Tg-SwDI/Usp16+/- of the three rescued pathways. These data suggest that USP16 may regulate neural precursor cell function in part through the BMP pathway.

Hoplodactylus duvaucelii sequencing reads (FastQ) - modern, historic and ancient

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied these methods to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historic/archival (1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-CT reconstructions. All 'large gecko' specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographic structuring within Hoplodactylus spp. highlighted the impacts of Late-Cenozoic biogeographic barriers, including the opening and closure of Pliocene marine straits, fluctuations in size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

Sequence-dependent model of genes with dual σ factor preference

Escherichia coli uses s factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single s factor, approximately 5% of them have dual s factor preference. The most common are those responsive to both s70, which controls housekeeping genes, and s38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'σ70+38 genes' are nearly as upregulated in stationary growth as 'σ38 genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to s38 and s70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.

Processed 12S fish eDNA sequences

This dataset contains fish eDNA sequences from the 12S mitochondrial gene. eDNA has been collected in 100 stations, 25 sites, in 5 tropical marine regions. Data collection was performed between 2017 and 2020. Raw sequences have been processed through a bioinformatic pipeline, merged, demultiplexed, dereplicated, clustered as OTUs (operational taxonomic units) and assigned to a taxa. The codes to analyse the data can be found at : <a href="https://github.com/virginiemarques/Global_eDNA">https://github.com/virginiemarques/Global_eDNA</a>. The data are used to study the patterns of tropical fish distributions across spatial scales, using two different methodologies, eDNA and visual census.

opencc-by-4.0Jul 2021View details →

Environmental effects of the December 2020 earthquake sequence near Petrinja, Croatia

Those files (Spreadsheet of observations of coseismic deformation features, Surface rupture shapefile) are in support of the paper submitted to Geophysical Journal International. The data have been collected by the coauthors of this paper, implemented in the files by them, and the database has been processed and verified by SB, AT, SP. The complete of authors of the paper is as follows: S. Baize1, S. Amoroso2,3, N. Belić4, L. Benedetti5, P. Boncio2, M. Budić4, F.R. Cinti3, M. Henriquet5, P. Jam&scaron;ek Rupnik6, B. Kordić4, S. Marku&scaron;ić7, L. Minarelli3, D. Pantosti3, S. Pucci3, M. &Scaron;pelić4, A. Testa2, S. Valkaniotis8, M. Vukovski4, J. Atanackov6, J. Barbača4, M. Bavec6, R. Brajkovič6, V. Brčić4, M. Caciagli3, B. Celarc6, R. Civico3, P.M. De Martini3, R. Filjak4, F. Iezzi2, A. Moulin5, T. Kurečić4, M. Métois9, R. Nappi3, A. Novak6,10, M. Novak6, B. Pace2, D. Palenik4, T. Ricci3 1 Institut de Radioprotection et de Sûreté Nucléaire, IRSN/PRP-ENV/SCAN/BERSSIN, 92262 Fontenay-Aux-Roses, France 2 Università “G. d'Annunzio” Chieti - Pescara, Via dei Vestini 31, 66100, Chieti, Italy 3 Istituto Nazionale di Geofisica e Vulcanologia, Via di Vigna Murata 605, 00143 Rome, Italy 4 Croatian Geological Survey, Department of Geology, Sachsova 2, Zagreb, 10000, Croatia 5 Aix Marseille Univ, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France 6 Geological Survey of Slovenia, GeoZS, Dimičeva ulica 14, 1000 Ljubljana, Slovenia 7 University of Zagreb, Faculty of Science, Department of Geophysics, Zagreb, Croatia 8 Department of Civil Engineering, Polytechnic School, Democritus University of Thrace, 67100 Xanthi, Greece 9 Laboratoire de Géologie de Lyon (LGLTPE), Université Claude Bernard Lyon 1, campus de La Doua, 69100 Villeurbane, France 10 University of Ljubljana, Faculty of Natural Sciences and Engineering, Department of Geology, Croatia

E.bieneusi sequence coverage

The supplementary file shows the sequence coverage of three E. bieneusi hypothetical proteins (B7XJ00, B7XHE2 and B7XIN4) detected in all seven individual plasma samples using Mascot search engine.

Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina

Background: Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. Results: We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes. Conclusion: This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.

Morphometric, gametic and parasitological data of clam Ameghynomia antiqua and DNAmt sequences of parasite

The clam Ameghynomia antiqua is a highly important resource for fisheries due to its high catches volume. It is the bivalve mollusk with the highest fisheries landings from natural beds on the Pacific coast of southern South America; however, studies of the reproductive conditions of this species are scarce and date back many years. The object of the present work was to evaluate the reproductive characteristics of the species, analysing its gametogenic and gonadal cycle, and reproductive indices, in fishery locations that present the natural beds with the highest fisheries catches, as well as parasite loads in the species. The gonads of the individuals were sampled monthly over a year and classified into one of three states called: "in development", "ripe" and "spawned". Synchrony between the sexes was observed in the indicators of the Gonadosomatic Index and Condition Index in each of the locations, although no synchrony was observed between locations. In the gametogenic cycle, the "ripe" state was observed in females in spring-summer, followed by rapid recovery to new development of the gonads; in males the "ripe" state was observed throughout the year. It was observed that males entered the "spawned" state one month ahead of females. The presence of digenean parasites in the state of metacercariae was detected in the gonads and mantle. No significant differences were found in the prevalence or intensity of infection when analysed by sex and month. The metacercariae were identified, by sequencing of three DNA regions, as belonging to the clade shared by species of the genus Parvatrema and close to the Gymnophalloides; both these genera belong to the family Gymnophallidae of the superclass Digenea. Infection was observed to reduce the gonadal tissue, in some cases causing castration. This is the first record of the presence of these parasites of A. antiqua, with genetic identification at genus level. These results are relevant for act proper management of this resource, which is important for fishing.

Urban Stream Environmental and Sequencing Datasets for Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams

The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams submitted to Applied and Environmental Microbiology.

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generate the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.

Image Sequence 2021

Images of fluorescing C+4 ions at a several velocities and times. (a) and (b) show the same velocity bins at two different times. (c) and (d) show the same time at two different velocity bins.

openagpl-3.0-or-laterDec 2021View details →

Simulated exome-sequencing data for a family study of lymphoid cancer

This repository contains all the data files for a simulated exome-sequencing study of 150 families ascertained to contain at least four members affected with lymphoid cancer. The simulated data can be found in the files section below. The files are: <ol> <li>SLiM_output.txt - contains the SLiM-simulated, exome-wide, SNV data generated under an American-admixture demographic model,  for the American-admixed sub-population only.</li> <li>SLiM_output_chr8&9.txt - contains the SLiM-simulated data above for all source populations as well as the American-admixed sub-population, but only for chromosomes 8 and 9.</li> <li>sample_info.txt - contains pedigree information of all the disease-affected individuals and individuals connecting them along a line of descent, for all 150 ascertained pedigrees.</li> <li>Genotypes.zip -  a zipfile that contains 22 text files of genotypes for each chromosome. The genotypes are for simulated single-nucleotide variants on the exome and are in gene-dosage format. </li> <li>SNVmaps.zip -  a zipfile that contains 22 text files giving the single-nucleotide variant information for each chromosome. </li> <li>familial_cRV.txt - contains the familial causal rare variants for all 150 ascertained pedigrees.</li> <li>study_peds.txt - contains the 150 pedigrees ascertained to contain four or more relatives affected with lymphoid cancer.</li> <li>PLINKfiles.zip -  a zipfile that contains PLINK .fam, .bim and .bed files for all 22 of the chromosomes.</li> </ol> All the scripts used to generate these data can be found in the GitHub repository archived at <a href="https://zenodo.org/record/6505385">https://zenodo.org/record/6505385</a> . We have also uploaded one intermediate .Rdata file, Chromwide.Rdata, to save the user substantial time when running the associated RMarkdown script for the simulation. We recommend loading Chromwide.Rdata into your R work-space rather than generating it from scratch.

Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence

Table S1. Base composition of chloroplast genome in P. forrestii, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from P. forrestii chloroplast genome, Table S4. Preferred codons in chloroplast genome of P. forrestii, Table S5. Long repeat sequences in the P. forrestii chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.