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BCO-DMO ERDDAP
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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
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| log in | [Kelletia kelletii: DNA and RNA sequence] - Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii (Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion) | Understanding the genomic characteristics of non-model organisms can bridge research gaps between ecology and evolution. However, the lack of a reference genome and transcriptome for these species makes their study challenging. Here, we complete the first full genome and transcriptome sequence assembly of the non-model organism Kellet's whelk, Kelletia kelletii, a marine gastropod exhibiting a poleward range expansion coincident with climate change. We used a combination of Oxford Nanopore Technologies, PacBio, and Illumina sequencing platforms and integrated a set of bioinformatic pipelines to create the most complete and contiguous genome documented among the Buccinoidea superfamily to date. Genome validation revealed relatively high completeness with low missing metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) and an average coverage of ∼70x for all contigs. Genome annotation identified a large number of protein-coding genes similar to some other closely related species, suggesting the presence of a complex genome structure. Transcriptome assembly and analysis of individuals during their period of peak embryonic development revealed highly expressed genes associated with specific Gene Ontology (GO) terms and metabolic pathways, most notably lipid, carbohydrate, glycan, and phospholipid metabolism. We also identified numerous heat shock proteins (HSPs) in the transcriptome and genome that may be related to coping with thermal stress during the sessile life history stage. A robust reference genome and transcriptome for the non-model organism K. kelletii provide resources to enhance our understanding of its ecology and evolution and potential mechanisms of range expansion for marine species facing environmental changes.\n\ncdm_data_type = Other\nVARIABLES:\nRun (unitless)\nAssay_Type (unitless)\nAvgSpotLen (unitless)\nBases (unitless)\nBioProject (unitless)\nBioSample (unitless)\nBioSampleModel (unitless)\nBytes (unitless)\nCenter_Name (unitless)\n... (29 more variables)\n | BCO-DMO | bcodmo_dataset_945292_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936069_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936069_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_936069_v1/ | public | [Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities] - Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022 (Collaborative Research: Microbes need frenemies: unveiling microbial relationships with protists and viruses that support deep-sea hydrothermal vent food webs) | This dataset is a collection of sample metadata, identified for all samples, and NCBI accession information for samples and sequence runs produced as part of the \"Microbes need frenemies\" project. This project examines trophic interactions among microbial eukaryotes, viruses, bacteria, and archaea at deep-sea hydrothermal vents using metagenomics and metatranscriptomics and characterizes these ecologically-significant interactions, such as mutualism, predator-prey, or virus-host. \n\nWe sequenced samples collected during the 2020 expedition AT42-22 to the Mid-Cayman Rise hydrothermal vent fields, as well as from the 2019 expedition NA108 to the Gorda Ridge and the 2022 expedition TN405 to the Axial seamount. Sequencing targeted archaea, bacteria, and viruses with metagenomics and microbial eukaryotes with metatranscriptomics. We plan to use these data to identify ecologically-significant interactions among protists, viruses, bacteria, and archaea, with a specific emphasis on microbial mortality via viral lysis and eukaryotic grazing. Archived samples were also included in the analysis.\n\ncdm_data_type = Other\nVARIABLES:\nSAMPLE_ID (unitless)\nSHORT_SAMPLE_ID (unitless)\nSAMPLE_NAME (unitless)\nLAB_NUM (unitless)\nCRUISE_ID (unitless)\nFIELD_REGION (unitless)\nYEAR (unitless)\nFIELD_YEAR (unitless)\nVENT (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nORIGIN_TYPE (unitless)\nORIGIN_DESCRIPTION (unitless)\nFRENEMIES_PROJ (unitless)\n... (11 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_936069_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_936069_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_936069_v1/index.htmlTable | https://www.bco-dmo.org/dataset/936069
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_936069_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_936069_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_936069_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914399_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914399_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_914399_v1/ | public | [Microbial eukaryotic diversity: Mid-Cayman Rise SRA dataset] - 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020 (Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists) | Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from two geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. Piccard and Von Damm vent fields are situated 20 km apart at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent-associated strains. This data adds to our growing knowledge of the biogeography of deep-sea microbial eukaryotes.\n\ncdm_data_type = Other\nVARIABLES:\nExperiment_Accession (unitless)\nExperiment_Title (unitless)\nOrganism_Name (unitless)\nInstrument (unitless)\nStudy_Accession (unitless)\nStudy_Title (unitless)\nSample_Accession (unitless)\nTotal_Size_Mb (Mb)\nTotal_Bases (bp)\nLibrary_Name (unitless)\nLibrary_Strategy (unitless)\nLibrary_Source (unitless)\nLibrary_Selection (unitless)\nVent_field (unitless)\nCollection (unitless)\nVent_name (unitless)\nDiveID (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_914399_v1/index.htmlTable | https://www.bco-dmo.org/dataset/914399
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_914399_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_914399_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_914399_v1 |