BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) (NCEI Accession 0278035)
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title: BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) (NCEI Accession 0278035)
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abstract: This dataset contains biological and survey - biological data collected on ARSV Laurence M. Gould during cruise LMG1401 on 2016-11-21. These data include genus and species. The instruments used to collect these data include Bioanalyzer and Inverted Microscope. These data were collected by Adrian Marchetti of University of North Carolina at Chapel Hill as part of the "Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators (Polar_Transcriptomes)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-06-11. The following is the text of the dataset description provided by BCO-DMO: BLASTp homology data from genes obtained in samples collected on LMG1411. Dataset Description: BLASTp homology data from genes obtained in samples collected on LMG1411. Diatom isolates were obtained from the Western Antarctic Peninsula surface waters.
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beginPosition: 2016-11-21
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supplementalInformation: Acquisition Description: Nine species of diatoms were isolated from the Western Antarctic Peninsula along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed using an Olympus CKX41 inverted microscope by single cell isolation with a micropipette (Anderson 2005). Diatom species were identified by morphological characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with the DNeasy Plant Mini Kit according to the manufacturer’s protocols (Qiagen). Amplification of the nuclear 18S rDNA region was achieved with standard PCR protocols using eukaryotic-specific, universal 18S forward and reverse primers. Primer sequences were obtained from Medlin et al. (1982). The length of the region amplified is approximately 1800 base pairs (bp). Pseudo-nitzschia species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of P. subcurvata was provided through sequencing of the 18S-ITS1-5.8S regions. Amplification of this region was performed with the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT (Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were edited using Geneious Pro software ( http://www.geneious.com , Kearse et al., 2012) and BLASTn sequence homology searches were performed against the NCBI nucleotide non-redundant (nr) database to determine species with a cutoff identity of 98%. Illumina TruSeq adapters and poly-A tails were trimmed from raw reads using the Fastx_toolkit clipper function. Fastq_quality_filter was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 80% of bases within a read meeting this quality score requirement. Any remaining raw sequences less than 50 base pairs in length were also removed. Merged files were assembled de novo using Trinity (Grabherr et al. 2011). The resulting assembly was filtered to remove contigs less than 200 bp in length. Trinity-assembled contigs which exhibited sequence overlap were grouped into isogroups which were then used for sequence homology searches (BLASTx E-value ≤ 10-4) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa 2006). Gene biogeographical distributions - 20 genes of interest were selected in the study to investigate the molecular basis of iron and light limitation in polar diatoms. Reference sequences for each of these genes were obtained from the F. cylindrus and P. tricornutum JGI genome portals and T. pseudonana and T. oceanica NCBI and GenBank repositories. Reference sequences were identified in the transcriptomes by translated nucleotide homology searches (tBLASTn) with an e-value cutoff of <10-5. A reciprocal tBLASTn homology search was performed for each transcriptome against the KEGG GENES database, using the single-directional best-hit method in the KAAS online tool to ensure consistent gene annotations (Moriya et al. 2007). Subsequently, reference sequences were identified in the MMETSP protein database by BLASTp (e-value <10-5) homology searches among the diatom transcriptomes. The transcriptomes and their associated latitude and longitude were obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the National Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts allowed global biogeographical distribution of key genes of interest to be mapped.
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linkage: ftp://ftp-oceans.ncei.noaa.gov/nodc/archive/arc0212/0278035/
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description: NCEI Accession 0278035 v1.1 was published.
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DateTime: 2023-05-11T05:04:07Z
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name: NCEI Accession 0278035 v1.1
description: published 2023-05-11T05:04:07Z
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acquisitionInformation: (MI_AcquisitionInformation)
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code: microscope
type: microscope
description: instrument is used in lab analyses A microscope is an instrument used to see objects that are too small for the naked eye.
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code: R/V Laurence M. Gould
description: Flag: United States of America Vessel Type: Research Vessel; Ice Breaker DOB: Dec 1997 IMO: 9137337 The RV Laurence M. Gould is an icebreaker used by researchers from the United States' National Science Foundation for research in the Southern Ocean. The vessel is named after Laurence McKinley Gould a widely recognized American scientist, who had explored both the Arctic and Antarctic. She was built in Louisiana to replace the RV Polar Duke.
instrument: (missing)
