Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay
Citation
MGnify (2019). Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Sampling event dataset https://doi.org/10.15468/mvatzn accessed via GBIF.org on 2020-01-21.Description
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454-pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting an overlapping region of the LSU rDNA D1/D2 region was used to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 µm) and two sampling depths (subsurface, at 1m, or deep-chlorophyll-maximum (DCM) at 23m).Sampling Description
Sampling
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454-pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting an overlapping region of the LSU rDNA D1/D2 region was used to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 µm) and two sampling depths (subsurface, at 1m, or deep-chlorophyll-maximum (DCM) at 23m).Method steps
- Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1
Taxonomic Coverages
Geographic Coverages
Bibliographic Citations
- Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C. 2013. Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. null vol. 22 - DOI:10.1111/mec.12108
Contacts
originatorSBR
metadata author
SBR
administrative point of contact
SBR