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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_954262_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_954262_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_954262_v1/ | public | [RECHARGE 2018 - 2020 Microbiome Data] - Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020 (Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature) | This dataset contains the complete sample information for the 16S rRNA gene V4 region amplicon sequencing data associated with the NCBI SRA accession from BioProject PRJNA994532. All raw sequencing data can be found at this publicly available NCBI SRA BioProject. \n\nThe associated samples were collected from an in situ coral manipulative experiment in Moorea, French Polynesia between 2018-2020 from Acropora retusa, Porites lobata, and Pocillopora spp. Data collection was a multi-university collaborative effort between the Vega Thurber Laboratory, at Oregon State University during the time of the experiment, and the Burkepile Community Ecology Laboratory at UC Santa Barbara. The experiment, conducted on the fore reef on the north shore of the island, evaluated the interaction of consumer pressure level (termed \"Herbivory\" in the dataset and in Vompe et al., 2023) and nutrient enrichment on coral microbiome composition and host success. The experiment also captured two severe and sequential marine heatwaves in 2019 and 2020. This experiment aimed to evaluate whether managing local inputs, including water column nutrient levels and fishing regimes, interacts with heat stress to affect coral success. Coral microbiomes were sampled as these microbial communities are known to interact with host health during heat stress. The data herein correspond to the microbiomes of the sampled corals.\n\ncdm_data_type = Other\nVARIABLES:\nSample (unitless)\nDate_MonthYear (unitless)\nCoral_Code (unitless)\nHerbivory (unitless)\nNutrients (unitless)\nPlot (unitless)\nTag (unitless)\nBatch (unitless)\nRun (unitless)\nAssayType (unitless)\nAvgSpotLen (unitless)\nBases (unitless)\n... (32 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_954262_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_954262_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_954262_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/954262
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_954262_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_954262_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_954262_v1 | |||
| log in | [Sequence metadata hatchery and restored reef oysters 2017-2020] - Sequence metadata for all sampled oysters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2017-2020 (CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems) | This dataset contains sequencing metadata for all 803 eastern oysters (Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657) sampled for genetic analysis and retained after SNP quality filtering as part of a multi-year oyster reef restoration experiment in Ninigret Pond, Rhode Island, USA. Oysters were sourced from four commercial hatcheries along the U.S. Atlantic coast (Maine, Massachusetts, New York, and Virginia) and sampled from hatchery source collections pre-experiment and from experimental restored reefs over time. Metadata are drawn from the NCBI Sequence Read Archive (BioProject PRJNA1280068), where the associated raw fastq files are publicly archived, and include sample identifiers, collection details, sequencing instrument/platform information, and SRA accession numbers linking each individual to its raw sequencing data. The primary genetic cluster assignment for each individual broadly correspond to the four commercial hatchery sources as described in the related individual genetic assignments dataset. A flag column indicates individuals excluded from downstream reef-level analyses for the associated manuscript, including those from reefs determined to have started as single-source reefs in fall 2018 and a small subset of individuals sampled outside the primary fall 2018 and fall 2020 time points.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\ntissue (unitless)\nacc (unitless)\nassay_type (unitless)\nbatch (unitless)\nbioproject (unitless)\nbiosample (unitless)\nbiosamplemodel (unitless)\nSRS (unitless)\ndatastore_filetype (unitless)\ndatastore_provider (unitless)\ndatastore_region (unitless)\nexperiment (unitless)\ngenotyped_individual (unitless)\n... (17 more variables)\n | BCO-DMO | bcodmo_dataset_1003894_v1 |