https://researchdata.se/sv/catalogue Search results sv Yearly monitoring programme of marine benthic fish communities along the Swedish west coast from 2002-2024 and ongoing. Since year 2013 a 16 mm mesh sized bottom trawl is used, prior to 2013 a 70 mm mesh size was used. Fish are identified to species, and their total weight and a subsample of lengths of each species are measured and recorded. Total weight of a selection of crustaceans and cephalopods species are also recorded. Sampling is carried out in quarter three. The monitoring programme is financed by the Swedish Agency for Marine and Water Management. Monitoring is performed by the Department of Aquatic Resources, Swedish University of Agricultural Sciences (SLU). Data is stored in the database FD2 by SLU. https://www.slu.se/om-slu/organisation/institutioner/akvatiska-resurser/databaser/databasen-for-fiske-i-havet/ Thu, 09 Apr 2026 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-7umtah https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-7umtah Sveriges lantbruksuniversitet Data curator This item contains analyses of gene homology between the Northern krill and nine other crustacean or krill species. The datasets span sequence files, orthology assessments and statistics about gene family evolution, divergence and molecular evolution. The species are associated with the following labels for file names and sequence headers: mnor = Meganyctiphanes norvegica (Northern krill) cqua = Cherax quadricarinatus (Australian red claw crayfish) dmag = Daphnia magna (water flea) eaff = Eurytemora affinis (copepod) hame = Homarus americanus (American lobster) hazt = Hyalella azteca (amphipod) phaw = Parhyale hawaiensis (amphipod) pmon = Penaeus monodon (Black tiger shrimp) pvan = Penaeus vannamei (Whiteleg shrimp) pvir = Procambarus virginalis (Marbled crayfish) Contents: - crustacean_homologs.non_redundant_datasets.tar.gz, contains an archive with peptide sequences for ten crustacean species, including those derived from the gene models in the Northern krill genome assembly. - crustacean_homologs.proteinortho_orthologs.tsv, results of the orthology inference among the peptide sequences using Proteinortho (standard Proteinortho format in TSV format). Documentation about the format is available on the site of the orignal tool: https://gitlab.com/paulklemm_PHD/proteinortho#readme - crustacean_homologs.proteinortho_1011_single_copy_orthologs_gblocks_unfiltered.tar.gz, multiple sequence alignments of n=1,011 single-copy orthologs between the ten species in FASTA format. - crustacean_homologs.proteinortho_1011_single_copy_orthologs_gblocks_filtered.tar.gz, as above but unreliable alignment positions have been deleted using Gblocks. - crustacean_homologs.swiftortho_gene_families.tar.gz, shared gene families inferred across the ten species using SwiftOrtho. - brh_mnor_esup_krill.peptide_sequences.fasta.tar.gz, peptide sequences in FASTA format used to detect reciprocal best hits between the Northern krill and the Antarctic krill. - brh_mnor_esup_krill.cds_sequences.fasta.tar.gz, the corresponding CDS nucleotide sequences in FASTA. - brh_mnor_esup_krill.gene_alignments.tar.gz, pairwise sequence-alignments and results of analysis of synonymous and non-synonymous sites and divergences (mixed formats). - brh_mnor_esup_krill.kaks_S_N_sites_dn_ds_dnds.tar.gz, summary tables of synonymous and non-synonymous sites and divergences (TSV files). - nrf6_alignments.tar.gz, multiple sequence alignments between sequences of the nrf-6 gene in the Northern krill, Antarctic krill and Whiteleg shrimp (FASTA). - wgd.datasets_and_results.tar, datasets and results used to study signatures of synonymous divergence (Ks) and whole genome duplication (wgd) among six crustaceans including the Northern krill. - crustacean_opsins.rstb20210289_si_004.fasta.with_krill.aligned.fasta, a protein alignment of crustacean opsin sequences in FASTA format, including the Northern krill. - crustacean_opsins.rstb20210289_si_004.fasta.with_krill.aligned.fasta.only_krill.fasta, a subset protein alignment of krill opsin sequences in FASTA format, including the Northern krill. - homeodomain.fasta.with_krill.fa.aligned.fa, alignment of animal Hox genes in FASTA format, including the Northern krill. - alkbh2.fasta.aligned.fasta.trimal, alignment of alkbh2 genes in FASTA format, including the Northern krill. - dnmt1.fasta.aligned.fasta.trimal, alignment of dnmt1 genes in FASTA format, including the Northern krill. - dnmt2.fasta.aligned.fasta.trimal, alignment of dnmt2 genes in FASTA format, including the Northern krill. - dnmt3.fasta.aligned.fasta.trimal, alignment of dnmt3 genes in FASTA format, including the Northern krill. - tet.fasta.aligned.fasta.trimal, alignment of tet2 genes in FASTA format, including the Northern krill. crustacean_homologs.non_redundant_datasets.tar.gz This archive contains one FASTA file per species, as well as one TSV file per species that translate between the simplified sequence names used in the FASTA file and the original NCBI sequence labels. crustacean_homologs.swiftortho_gene_families.tar.gz This archive contains multiple files: - all_matches.out = a TSV output file from SwiftOrtho with homology information based on all vs. all hits. The format is similar to tabular BLAST output ("blastp -m8") but also contains sequence lengths in the last two columns. The SwiftOrtho format is documented on the site of the original tool: https://github.com/Rinoahu/SwiftOrtho - all_matches.out.30_30.orth.apc = line by line gene family assignments using the Affinity Aropagation APC algorithm (TSV). - all_matches.out.30_30.orth.apc.table.ALL.csv = the above gene family assignment but written as a count data file for CAFE. The format is described on the site of the original tool: https://github.com/hahnlab/CAFE5 - all_matches.out.30_30.orth.apc.table.mnor.csv, as above but filtered to only contain gene families with at least one gene in the Northern krill. - all_matches.out.30_30.orth.apc.table.mnor_dmag.csv, as above but filtered to only contain gene families with at least one gene in the Northern krill and the water flea. brh_mnor_esup_krill.gene_alignments.tar.gz This file contains pairwise sequence alignments for n=13,373 putatively orthologous genes between the Northern krill (mnor) and the Antarctic krill Euphausia superba (esup), as well as associated files to analyse sequence composition and divergence. The orthologs were detected using reciprocal best hit with BLASTP and gene has its own directory. Each directory contains: - seq.aa.fasta = the two peptide sequences encoded by the homologus genes - seq.nt.fasta = the corresponding nucleotide sequences - seq.aa.fasta.ginsi.fasta = pairwise alignment of peptide sequences - seq.aa.fasta.ginsi.fasta.pal2nal.fasta = aligned nucleotide sequences fitted using PAL2NAL (also includes an additional log file) - seq.aa.fasta.ginsi.fasta.pal2nal.fasta.nogaps.fasta = alignment after removing all columns with gaps. - seq.aa.fasta.ginsi.fasta.pal2nal.fasta.nogaps.fasta.axt = alignment in AXT format for KaKs Calculator - seq.aa.fasta.ginsi.fasta.pal2nal.fasta.nogaps.fasta.axt.YN.tsv = output from KaKs Calculator, including synonymous and non-synonymous sites and substitutions (also includes an additional log file) wgd.datasets_and_results.tar.gz This archive contains one directory with wgd data and results of analyses per species (n=6): - Meganyctiphanes norvegica - Homarus americanus - Penaeus monodon - Hyalella azteca - Eurytemora affinis - Daphnia magna The files include the coding sequences used to study wgd patters (FASTA-format), gene family clustering output (MCL) and the Ks distributions and mixture model tests. The details of these files are documented on the site of the orignal tool: https://wgd.readthedocs.io/en/latest/methods.html Wed, 27 Mar 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22792943 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22792943 Uppsala universitet Andreas Wallberg Per Unneberg Pilot short-read genome assembly of one single adult barnacle, Balanus improvisus (=Amphibalanus imrpovisus), used to estimate genome size and heterocygosity. Bi01.clean.fa.gz is the final assembly with contaminations etc removed. Alm Rosenblad et al., Marine Biotechnology 2021 Abstract Barnacles are key marine crustaceans in several habitats and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in 4-fold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), %), which might increase the risk that barnacle populations evolve resistance towards antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies. Fri, 16 Apr 2021 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-14339153 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-14339153 Göteborgs universitet Magnus Alm Rosenblad Björn Nystedt This item holds multiple gene and repeat model and annotation files, including coordinates in GFF/GTF formats, TXT/TSV table and sequences in FASTA format. It also contains some accessory RNA-seq gene resources, such as Trinity-assembled transcripts and Nanopore cDNA sequences that were used at various stages of assembly and annotation. Coordinates refer to the main genome assembly reference sequence (1.m_norvegica.main_w_mito.fasta) but focus on the nuclear genome assembly and rarely include features of the mitochondrial assembly. Mitochondrial annotations are provided separately (see below). Contents: - trinity_transcripts.tar.gz, an archive with n=573,869 RNA transcripts that have been assembled with Trinity using Illumina RNA-seq data in FASTA format. - trinity_transcript.16509_single_isoforms.cds.fasta.tar.gz, a subset of 16,509 single (longest) isoform of putatively protein-coding transcripts used to assess genome assembly metrics such as duplication and base-level error. Sequences are in FASTA format. - nanopore_cDNA.representative_sequences_vsearch.tar.gz, n=25,484 cDNA Nanopore sequence reads used to filter gene models and scaffold the genome. - annotations.all_genes_and_isoforms.redundant.tar.gz, an archive with all (n=202,138) gene models and isoforms/alternative splice variants, including also non-protein coding genes. - annotations.protein_coding_gene_models.non_redundant.gff3, a non-redundant (i.e. single-isoform) set of putative protein-coding gene bodies (n=42,227) in standard GFF3 format. - annotations.protein_coding_gene_models.non_redundant.CDS.fasta, the matching set of putative protein-coding genes in FASTA format (CDS nucleotide sequences). - annotations.protein_coding_gene_models.non_redundant.PEP.fasta, the matching set of putative protein sequences in FASTA format (PEP peptide sequences). - annotations.protein_coding_gene_models.non_redundant.PEP.fasta.BLAST.DROSOPHILA.tsv.tar.gz, output from BLASTP analyses between Northern krill and Drosophila peptide sequences (BLAST outfmt 6). - annotations.protein_coding_gene_models.non_redundant.PEP.fasta.EnTAP.final_annotations_lvl1.tsv, main output from EnTAP functional annotations of protein coding genes. - annotations.protein_coding_gene_models.non_redundant_added_stop_codons.gff, non-redundant protein-coding models as above, but missing stop-codons have been added if detected in the reference genome assembly (GFF format). - annotations.protein_coding_gene_models.non_redundant_added_stop_codons.CDS.fasta, but missing stop-codons have been added if detected in the reference genome assembly (FASTA format). - mitochondrion.tar.gz, an archive with gene coordinates and sequences of tRNAs, rRNAs, protein-coding genes and repeat features on the mitochondrial chromosome, as inferred using MITOS2. Files are standard BED/GFF/TSV/TXT/FASTA files and more information about formats can be found on the site for the original tool: http://mitos2.bioinf.uni-leipzig.de/help.py - annotations.repeat_library.fasta, a custom set of n=10,909 non-redundant repeat sequences in FASTA format that were used to annotate the genome for repeats using RepeatMasker. - annotations.repeats_across_the_genome_repeatmasker.tbl, the standard RepeatMasker masking overview output table. - annotations.repeats_across_the_genome_repeatmasker.out.tar.gz, the full set of masked repeats and their coordinates across the genome. trinity_transcripts.tar.gz This archive contains the assembled transcripts assembled from RNA-seq data produced from six RNA extractions/tissues of the reference specimen. There are three FASTA files: - trinity_transcripts.all_genes_and_isoforms.fasta = all assembled transcripts (n=573,869) - trinity_transcripts.metazoan_genes_and_isoforms.CDS.fasta = a subset of n=60,677 assembled and putatively coding transcripts with best hits against Metazoan sequences (CDS nucleotide sequences) - trinity_transcripts.metazoan_genes_and_isoforms.PEP.fasta = the n=60,677 corresponding peptide sequences. nanopore_cDNA.representative_sequences_vsearch.tar.gz This archive contains putatively full-length cDNA reads in three FASTA files: - clusters.fa = VSEARCH cluster representatives (i.e. cluster centroids with low error rates) that retain the original Nanopore sequence headers (n=25,484) - clusters.renamed.fa = as above, but renamed with simple incrementing headers. - clusters.renamed.min_500bp.fa = as above, but only reads longer than 500 bp (n=24,632). These reads were used to scaffold the genome. annotations.all_genes_and_isoforms.redundant.tar.gz This archive contains gene models in four files: - annotations.all_genes_and_isoforms.redundant.gtf, coordinates in GTF format - annotations.all_genes_and_isoforms.redundant.gff3, coordinates in GFF3 format - annotations.all_genes_and_isoforms.redundant.fasta, sequences in FASTA format - annotations.all_genes_and_isoforms.redundant.transcripts.tsv, a TSV table with three fields specifying: 1) the final name of the isoform/splice variant; 2) the name of the gene model it belongs to; 3) the original name the isoform. These models were consolidated into loci using GFFCOMPARE from multiple sources of data, including RNA and comparative data. The names of the original isoforms indicate source: - STRG = HISAT/STRINGTIE RNA-seq gene model. Tagged "REF_STRG" in the final gene model. - mRNA = Assembled Trinity transcript. Tagged "REF_TRIN" in the final gene model. - COMPARATIVE_SPALN = Comparative model derived other crustaceans. GFF and GTF format specifications are available here: https://www.ensembl.org/info/website/upload/gff.html https://www.ensembl.org/info/website/upload/gff3.html annotations.protein_coding_gene_models.non_redundant.(gff3|CDS.fasta|PEP.fasta) These files contains a filtered set of the "best" model isoform of each locus (n=42,227) in total, which were determined by comparison to NCBI RefSeq. These models were used to annotate SNPs, infer homology/orthology, gene family evolution and molecular evolution. annotations.repeat_library.fasta This FASTA file contains the representative and non-redundant template repeat sequences that were used to annotate the Northern krill genome for interspersed repeats. The sequence headers indicate several aspects of each repeat. Example: "seq_c_98391_5186_12351_FIN_ReC99C#LTR/Pao" This indicates that the template is: - located on sequence seq_c_98391 with start/stop coordinates 5186/12351 - originally detected using LTR_Finder ("FIN") - classified as "LTR/Pao" using RepeatClassifier ("ReC") - has 99% identity between the 5' and 3' LTRs ("99") and was considered complete, with respect to the expected protein domains detected along the repeat. Additional tags and nomenclature are described in the paper methods. Wed, 27 Mar 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22786925 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22786925 Uppsala universitet Andreas Wallberg Per Unneberg This item holds one major gzipped tar archive that contains 20 nested tar archives, each of which containing reference transcriptomes and associated metadata for one species of krill (20 species in total). Archive: krill.transcriptomes.tar.gz Contents of major archive (FILE,TAG,SPECIES,SIZE): - earm.transcriptomes.tar,earm,Euphausia similis var. armata,491.6M - ecry.transcriptomes.tar,ecry,Euphausia crystallorophias,89.7M - edin.transcriptomes.tar,edin,Euphausia distinguenda,496.5M - efri.transcriptomes.tar,efri,Euphausia frigida,345.2M - elam.transcriptomes.tar,elam,Euphausia lamelligera,515.9M - elos.transcriptomes.tar,elos,Euphausia longirostris,234M - emuc.transcriptomes.tar,emuc,Euphausia mucronata,360.4M - epac.transcriptomes.tar,epac,Euphausia pacifica,357.1M - erec.transcriptomes.tar,erec,Euphausia recurva,114.8M - esim.transcriptomes.tar,esim,Euphausia similis,417.9M - espi.transcriptomes.tar,espi,Euphausia spinifera,425.1M - esup.transcriptomes.tar,esup,Euphausia superba,520.6M - etri.transcriptomes.tar,etri,Euphausia triacantha,396M - eval.transcriptomes.tar,eval,Euphausia vallentini,635.1M - mnor.transcriptomes.tar,mnor,Meganyctiphanes norvegica,469M - nmeg.transcriptomes.tar,nmeg,Nematoscelis megalops,429M - tine.transcriptomes.tar,tine,Thysanoessa inermis,594.6M - tlon.transcriptomes.tar,tlon,Thysanoessa longicaudata,328.8M - tmac.transcriptomes.tar,tmac,Thysanoessa macrura,253.4M - trac.transcriptomes.tar,trac,Thysanoessa raschii,231.2M Contents of nested archives: Each nested tar archive contains the follow set of files (the "TAG" prepends the filenames according to the list of species tags above): TAG. trinity.fasta The full Trinity transcriptomem, including non-coding transcripts and alternative isoforms TAG.trinity.longest_isoforms.fasta.renamed.list.tsv: A TSV table to translate between original Trinity transcript sequence names (field 3) and names used throughout the analyses (field 2). This table contains the longest isoforms, i.e. the resulting transcripts after removing redundant shorter isoforms. - field 1: number - field 2: species-specific transcript sequence names used in analyses. The sequence name follow the format "TAG_NUMBER" for non-coding transcripts and "TAG_NUMBER_OTHER_NUMBER" for coding transcripts (the last number indicates which reading-frame was selected by transdecoder as the best). - field 3: original Trinity transcript sequence names TAG.trinity.longest_isoforms.coding.fasta The filtered transcriptome, including only the longest isoform of each coding transcript. TAG.trinity.longest_isoforms.coding.fasta.transdecoder.gff3 A GFF coordinate file that specifies where along the coding transcripts features such as CDS, UTRs start and stop. TAG.trinity.longest_isoforms.fasta.transdecoder.cds.fasta The CDS of the open reading frame of coding transcripts, as specified by the TAG.trinity.longest_isoforms.coding.fasta.transdecoder.gff3 GFF file and the TAG.trinity.longest_isoforms.coding.fasta file. TAG.trinity.longest_isoforms.fasta.transdecoder.pep.fasta The corresponding peptide sequence of encoded by each CDS. The GFF files follow the GFF3 standard: https://www.ensembl.org/info/website/upload/gff3.html The FASTA files follow the FASTA standard: https://www.ncbi.nlm.nih.gov/genbank/fastaformat/ Note: Compared to the files used in analyses, these files have been edited to reflect the species names and abbreviations used in publication figures. Thu, 19 Oct 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22722361 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-22722361 Uppsala universitet Andreas Wallberg This item contains a gzipped archive with ~13,000 orthogroups used to study molecular evolution in this project. Archive: krill.orthogroups.tar.gz Contents of archive (FILE,SIZE,SPECIES,SAMPLES,SNPs): - krill.proteinortho.tsv - the primary output table from Proteinortho. Describes which protein sequences from which species belong to the same orthogroup. Format according to the standard output of the program. - krill.proteinortho.tsv.seqs.csv - a processed table that also contains the actual sequences line by line (see below). - the alignments directory, which contains all OGs in unaligned and aligned files in FASTA format (see below). Format of the krill.proteinortho.tsv.seqs.csv table The fields are: - NR = orthogroup number - ORTHO_GROUP = orthogroup ID - N_SPECIES = the number of species - N_GENES = the number of genes/sequences in this orthogroup - N_MATCHING[o] = number of sequences matching outgroup species for this orthogroup - N_NON_MATCHING = number of sequences matching ingroup species for this orthogroup - HEADER = the name of this particular sequence - SEQ = the protein sequence Contents of the alignments directory Each orthogroup is represented by up to four FASTA files: - OG*.cds.ginsi.fasta.orig = the original, unaligned and unfiltered sequences - OG*.cds.ginsi.fasta = the aligned and filtered sequences - OG*.cds.ginsi.fasta.without_cold_euphausia.fasta = the aligned and filtered sequences after removing cold-associated Euphausia species - OG*.cds.ginsi.fasta.without_cold_thysanoessa.fasta = the aligned and filtered sequences after removing cold-associated Thysanoessa species Thu, 19 Oct 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-24039510 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-24039510 Uppsala universitet Andreas Wallberg Fenotypisk växtdata och herbivory data från åtta Solanum dulcamara populationer i fyra habitat i södra Sverige, och leddjursdata från fem av dessa population insamlade med skålfällor och klibbiga fällor. De fenotypiska växtdata inkluderar mått på tillväxt och reproduktion. Herbivoridata inkluderar mått på förlorad bladyta. Leddjursdata är uppdelade på olika taxa. Thu, 03 Sep 2026 12:19:13 GMT https://researchdata.se/sv/catalogue/dataset/2026-144 https://researchdata.se/sv/catalogue/dataset/2026-144 Sveriges lantbruksuniversitet Åsa Lankinen Kristin Aleklett