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opencc-by-4.0Oct 2023View details →

Next-generation Sequencing Data Associated with "Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches"

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opencc-by-4.0Nov 2023View details →

Short and Long Read Sequences from VIM-1 producing (Klebsiella pneumoniae test-dataset)

Creation of a downsized version of the long and short reads data of VIM-1 producing Klebsiella pneumoniae. Samples were obtained from the Hospital Infanta Cristina (Badajoz, Spain) on October 11th, 2019. - Long read data: Oxford Nanopore Technology (A1403KPN.fastq.gz).- Short read data : Illumina (A1403KPN_R2_filtered.fastq.gz && A1403KPN_R2_filtered.fastq.gz)

Raw sequencing data and ngsfilters for snow track eDNA samples

Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present the first successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR) and, for brown bear, a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear samples (5/7) than for wolf (7/10) and lynx (4/9), but locus genotyping success was greater for brown bear (0.88). Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success are needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA–based individual and population-level studies.

opencc-by-4.0Sep 2023View details →

TAGET: A toolkit for analyzing full-length transcripts from long-read sequencing

Polished transcripts of COLO829 from the PacBio platform. The original web link: https://downloads-ap.pacbcloud.com/public/dataset/Melanoma2019_IsoSeq/PolishedMappedTranscripts/before-SQANTI2filter/.

openOct 2023View details →

ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing applied to identify small and large translated ORFs

ProTInSeq is a novel -omics technique designed to characterize proteomes by using DNA ultra-deep sequencing. The technique is based on transposons engineered to have a positive or negative protein selection marker expressed when the transposon is inserted in-frame into a protein-coding gene. In the genome-reduced bacterium Mycoplasma pneumoniae, ProTInSeq identifies 80% of known expressed proteins, as well as 5 new open reading frames (ORFs; >100 amino acids); and 153 novel small ORF-encoded proteins (SEPs; ≤100 aa) that represent up to 18% of this bacterium’s proteome. ProTInSeq can be used to detect translational noise, for protein quantification and to provide insight into functional protein aspects such as relative half-life, stability, and membrane topology. Herein, we describe a methodology that can be easily implemented in any living system and allows the deep understanding of proteomes and more importantly the identification of small proteins by DNA ultra-sequencing. We include the following files: - processed_inscalling.zip: output obtain after running FASTQINS transposon calling tool over the datasets found at <a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10380?key=5f54209d-ce59-490a-9bcd-7084e9c619ee">https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10380?key=5f54209d-ce59-490a-9bcd-7084e9c619ee</a>. This include every genome position in M. pneumoniae, the number of times an insertion has been mapped to that position and the total read count value. - separated_library_metrics.zip: insertion and read count processed from processed_inscalling files associated to every ORF  and intergenic region in M. penumoniae. Columns include frame measured (0 - whole gene, 1 - in-frame, 2 and 3 for following positions) and metric. Metrics account for number insertions in-frame (I), read count (R), linear density from non-coding regions used in the Poisson evaluation (rNC), probability measured (sfNC) and a binary for prediction (pred; 0 - no significant, 1 - significant). - allmetrics.xlsx: merged table with the combination of results from separated_library_metrics.zip tab-delimited files. - selective_metrics_allannotations.xlsx:  this table includes all the available information about the 30,112 sequences that could encode for a coding sequence in M. pneumoniae. For each identifier (column B), we include coordinates information and nucleotide and amino acid length information (columns C-H). Column I includes the gene name when the entry is found annotated in M. pneumoniae. Localization and function are described in columns J and K. Column L includes the operon number in which the annotation would be expressed. We also included transcription-related information average expression (column M; as log2(gene read count/gene length) and estimated average RNA copies per cell (column N) considering 4 RNA sequencing samples covering different growth times (6, 24 and 48 hours, ArrayExpress identifier E‐MTAB‐6203). Column O accounts for the number of mass spectrometry experiments detecting that entry (to a maximum of 116) and column P accounts for the total number of unique tryptic peptides detected. This comes <a href="https://paperpile.com/c/BImj5N/eljz">[5]</a>, available for 12,426 sequences that present an amino acid length ≥19 (from 116 mass spectrometry experiments, ID PRIDE: PXD008243). Columns Q to T recapitulate protein copies per cell under different conditions (overall, extracting with urea, extracting with SDS and mean, respectively). Column U includes half-lives of the proteins. Columns V and W describe the reference density of insertion and essentiality assigned in previous studies. Column X-AA includes the predicted RanSEPs score, ribosome binding site presence, homology into seven groups: 0—no hits passed the thresholds defined; 1—conserved with an annotated function; 2—conserved as an annotated SEP in NCBI but no associated function; 3—conserved in a different species but target and homologous sequence not found in NCBI; 4—sequence is completely or partially (> 75%) repeated ≥ 3 times in the reference genome; 5—potential pseudogene; and 6—to depict those annotations that are found in the reference NCBI annotation file. , and function expected by homology, respectively. Columns AB to AD cover the output provided by Phobius, including the number of transmembrane segments, presence of signal peptide and transmembrane topology predicted by TM-HMM. Column AE includes the complex information where 1 implies that entry is functional as a monomer, 2 as dimer, and so on. Finally, columns AF-AH will be 1 if the protein is a Lon protease target, a lipoprotein, and/or a truncated gene or pseudogene, respectively, 0 otherwise. Following columns include for every sample presenting selective insertion rates in-frame using the following identifiers separated by underscores: marker (BarnB, Cm or Ery), type (control-AC or selection-BD, antibiotic concentration, sample replicate, frame measured, metric. Metrics account for number insertions in-frame (I), read count (R), linear density from non-coding regions used in the Poisson evaluation (rNC), probability measured (sfNC) and a binary for prediction (pred; 0 - no significant, 1 - significant). Last columns combine the number of samples each annotation has been identified. Notice for barnase library the results need to be interpreted considering it is a negative selection marker inverting the 0 and 1 meaning.

DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2

As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the ND2 sequences; a single haplotype was identified within the Cyt b sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species.

openNov 2023View details →

Multiple sequence alignments: Detection and isolation of a new member of Burkholderiaceae‑related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales

Methods:Nucleotide sequences were aligned independently for each region using MAFFT v7.212 (Katoh and Standley, 2013). The obtained alignment blocks were subject to Gblocks 0.91b (Castresana, 2000) to remove poorly aligned positions with the relaxed selection setting described in Talavera & Castresana (2007) using the following parameters (-t = d -b2 = 9 -b3 = 10 -b4 = 5 -b5 = h). After automatically removing gaps, the alignment blocks were viewed using MEGA 6.06 software (Tamura et al., 2013) and poorly aligned positions at either end of the alignments were removed manually. Pairwise distances of the nucleotide sequences (ITS2, ITS1-5.8S-ITS2, LSU, and tef1) of the ex-type strains of seven Saksenaea spp. and the representative isolate S. boninensis Sak4 were calculated by MEGA 6.06 software (Tamura et al. 2013). Multiple sequence alignment of 16S rRNA gene of the family Burkholderiaceae was prepared for the phylogeny of a bacterial endosymbiont. Multiple sequence alignments of  ITS, LSU, and tef1 genes of Saksenaea spp. (Mucorales) were separately prepared for the phylogeny of a fungal host. Concatenated dataset of these genes were also prepared. All nucleotide sequences were retrieved from GenBank (See "Sequence_ID.csv" and taxon names of each alignment).   Description of files:A. Phylogeny of the family Burkholderiaceae (Bacterial endosymbiont):1. Burkholderiaceae_16S_RAW.fastaNon-aligned dataset of 16S rRNA gene of the family Burkholderiaceae. 2. Burkholderiaceae_16S_aligned.fastaAligned dataset of 16S rRNA gene of the family Burkholderiaceae. B. Phylogenies of Saksenaea spp. (Fungal host):1. Sequence_ID_v2.csvTaxon names, accession numbers, and sequence ID for the concatenated multiple sequence alignment are listed. 2. Saksenaea_ITS_RAW_v2.fastaNon-aligned dataset of ITS1-5.8S-ITS2 region of Saksenaea spp.   3. Saksenaea_ITS_aligned_v2.fastaAligned dataset of ITS1-5.8S-ITS2 region of Saksenaea spp. Only used for ITS1-5.8S-ITS2 phylogeny. 4. Saksenaea_LSU_RAW_v2.fastaNon-aligned dataset of LSU gene region of Saksenaea spp.   5. Saksenaea_LSU_aligned_v2.fastaAligned dataset of LSU gene region of Saksenaea spp. Only used for LSU phylogeny. 6. Saksenaea_tef1_RAW_v2.fastaNon-aligned dataset of tef1 gene region of Saksenaea spp.   7. Saksenaea_tef1_aligned_v2.fastaAligned dataset of tef1 gene region of Saksenaea spp. Only used for tef1 phylogeny. <Concatenated dataset 1 (ITS2, LSU, tef1)>8. Saksenaea_ITS2_for_concatenated_RAW_v2.fastaNon-aligned dataset of ITS2 region of Saksenaea spp. used for preparation of a concatenated dataset 1. 9. Saksenaea_ITS2_for_concatenated_aligned_v2.fastaAligned dataset of ITS2 region of Saksenaea spp. used for preparation of a concatenated dataset 1. 10. Saksenaea_LSU_for_concatenated_RAW_v2.fastaNon-aligned dataset of LSU gene region of Saksenaea spp. used for preparation of concatenated datasets 1 and 2. 11. Saksenaea_LSU_for_concatenated_aligned_v2.fastaAligned dataset of LSU gene region of Saksenaea spp. used for preparation of concatenated datasets 1 and 2. 12. Saksenaea_tef1_for_concatenated_RAW_v2.fastaNon-aligned dataset of tef1 gene region of Saksenaea spp. used for preparation of concatenated datasets 1 and 2. 13. Saksenaea_tef1_for_concatenated_aligned_v2.fastaAligned dataset of tef1 gene region of Saksenaea spp. used for preparation of concatenated datasets 1 and 2. 14. Saksenaea_ITS2_LSU_tef1_concatenated_dataset1.fastaConcatenated dataset of three multiple sequence alignments (9, 11, and 13). This concatenated dataset was used for the main phylogeny of Saksenaea spp. <Concatenated dataset 2 (ITS1-5.8S-ITS2, LSU, tef1)>15. Saksenaea_ITS_for_concatenated_RAW_v2.fastaNon-aligned dataset of ITS1-5.8S-ITS2 region of Saksenaea spp. used for preparation of a concatenated dataset 2. 16. Saksenaea_ITS_for_concatenated_aligned_v2.fastaAligned dataset of ITS1-5.8S-ITS2 region of Saksenaea spp. used for preparation of a concatenated dataset 2.Blank sequences were inserted for five isolates of Saksenaea longicolla after the alignment. 17.Saksenaea_ITS_LSU_tef1_concatenated_dataset2.fastaConcatenated dataset of three multiple sequence alignments (15, 11, and 13). This concatenated dataset was used for the main phylogeny of Saksenaea spp. C. Pairwise distances of the ex-type strains of Saksenaea spp.1. Saksenaea_ITS_type_RAW.fastaNon-aligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of Saksenaea spp. 2. Saksenaea_ITS2_type_aligned.fastaAligned dataset of ITS2 region of the ex-type strains of Saksenaea spp. 3.Saksenaea_ITS_type_aligned.fastaAligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of Saksenaea spp. without Saksenaea longicolla. 4. Saksenaea_LSU_type_RAW.fastaNon-aligned dataset of LSU gene region of the ex-type strains of Saksenaea spp. 5. Saksenaea_LSU_type_aligned.fastaAligned dataset of LSU gene region of the ex-type strains of Saksenaea spp. 6. Saksenaea_tef1_type_RAW.fastaNon-aligned dataset of tef1 gene region of the ex-type strains of Saksenaea spp. 7. Saksenaea_tef1_type_aligned.fastaAligned dataset of tef1 gene region of the ex-type strains of Saksenaea spp.

Nematostella vectensis full length opsin sequences and transcriptomes

Opsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g. jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g. corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemone Nematostella vectensis. We analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We identified 29 opsins from N. vectensis (NvOpsins) with high confidence, using transcriptomic and genomic datasets. We found that lineage-specific opsin duplications are common across Cnidaria, with anthozoan lineages exhibiting among the highest numbers of opsins in animals. To establish the putative photosensory function of NvOpsins, we identified canonically conserved protein domains and amino acid sequences essential for opsin function in other animal species. We show high sequence diversity among NvOpsins at sites important for photoreception and transduction, suggesting potentially diverse functions. We further examined the spatiotemporal expression of NvOpsins and found both dynamic expression of opsins during embryonic development and sexually dimorphic opsin expression in adults. These data show that lineage-specific duplication and divergence have led to expansive diversity of opsins in eyeless cnidarians, suggesting opsins from these animals may exhibit novel biochemical functions. The variable expression patterns of opsins in N. vectensis suggest opsin gene duplications allowed for a radiation of unique sensory cell types with tissue- and stage-specific functions. This diffuse network of distinct sensory cell types could be an adaptive solution for varied sensory tasks experienced in distinct life history stages in anthozoans.

Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant Cryptomeria species in Japan (C. japonica) and Southeastern China (C. japonica var. sinensis). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of Cryptomeria was moderate (Ho = 0.217, He = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (FST = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of Cryptomeria in East Asia. Our results shed light on the speciation processes of Cryptomeria and provide a reference for the conservation of this species.

Varieties SNPs-based sequencies

This is not a consensus sequencing. SNPs for one sample per file were used. Pinot noir was used as a reference.

MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects

This dataset represents all results files described in the paper 'MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects'.

Varieties SNPs-based sequencies (3)

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Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress

This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.

ABodyBuilder2 predicted structures of paired antibody sequences from Observed Antibody Space.

We used ABodyBuilder2 (https://doi.org/10.1038/s42003-023-04927-7) to model ~1.5M paired antibody structures from paired antibody sequences in Observed Antibody Space (https://opig.stats.ox.ac.uk/webapps/oas/oas_paired/). We have save the structures in folders and sub folders that correspond to the OAS files they came from. Parent folders are named according to study. Within each parent folder are sub folders names according to the files (named by SRA ID) containing sequences. Each structure is then named with the parent file followed by the row number from this file.

opencc-by-4.0Feb 2023View details →

gapseq sequence database

The repository contains the protein sequences used by gapseq [https://github.com/jotech/gapseq] to predict the presence of metabolic reactions and to construct metabolic models.

Non-Perennial rivers and streams under hydrological stress – comparing the effectiveness of amplicon sequencing and digital microscopy for diatom biodiversity appraisal

ABC is project leader, data collector, contact person, etc.

Dataset for the ancestral sequence reconstruction of NRC3

Please refer to the material_and_method.pdf to check how we generated each file. 01_NRCH_cds_23-03-03.fastaFASTA file containing the nucleotide sequences of 2341 NRC helper sequences extracted from 124 Solanaceae NLRome dataset [1] and 20 NRC helper sequences from Adachi et al. 2023 [2]. 02_NRCH_cds_23-03-03.min2400max2800.fastaFASTA file containing the nucleotide sequences of 1753 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp. 03_NRCH_cds_23-03-03.min2400max2800.uniq.fastaFASTA file containing the nucleotide sequences of 1116 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp and to remove duplicates. 04_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.fastaFASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates. 05_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fastaFASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates and after alignment with MAFFT. 06_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta.treefileNewick file containing the phylogenetic tree of the 1116 NB-ARC domains of NRC helpers reconstructed with FastTree. 07_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.fastaFASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades. 08_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.aln.fastaFASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades after alignment with MAFFT. 09_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fastaFASTA file containing the 324 full-length nucleotide sequences of the NRC1/2/3/X clades threaded onto the protein alignment with MAFFT. 10_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta.treefileNewick file containing the phylogenetic tree of the 324 full-length nucleotide sequences of the NRC1/2/3/X clades reconstructed with IQ-TREE. 11_FastML_NRC123X.zipZip file containing the FastML results for the ancestral sequence reconstruction of the NRC1/2/3/X clades. 1. Sugihara, Y., Toghani, A., Kamoun, S., & Kourelis, J. (2023). NLRome dataset from 124 genomes of plants in the Solanaceae family. Zenodo. https://doi.org/10.5281/zenodo.103543502. Adachi, H., Sakai, T., Harant, A., Pai, H., Honda, K., Toghani, A., Claeys, J., Duggan, C., Bozkurt, T. O., Wu, C., & Kamoun, S. (2023). An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana. PLOS Genetics, 19(1), e1010500. https://doi.org/10.1371/journal.pgen.1010500

A root-specific NLR network confers resistance to plant parasitic nematodes - genomic sequences and annotations

Sequence and annotation data associated with "A root-specific NLR network confers resistance to plant parasitic nematodes"

Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection

Processed data (feature-by-sample matrices) of non-disruptive bisulfite-free methylation sequencing for cfDNA samples from 4 clinical cohorts (Cohort 1, Cohort 2, Cohort 3, and cfTAPS dataset). Codes used to repeat the results in our paper can be found https://rpubs.com/LiYumei/926228 and https://github.com/ChaorongC/MESA.