Dataset
OBIS Secretariat Open in mapper Explore occurrences
Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments.
Published: September 20, 2022 at 12:42
License: This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY) 4.0 License
URL: https://hosted-datasets.gbif.org/mgnify/MGYS00002531.zip
Contacts:
MBL
MBL
| Field | Missing | Invalid | |
|---|---|---|---|
| coordinateUncertaintyInMeters | 1,894 |
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| eventDate | 1,894 |
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| maximumDepthInMeters | 1,246 |
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| minimumDepthInMeters | 1,246 |
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| occurrenceStatus | 1,894 |
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| scientificNameID | 1,894 |
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The OBIS data quality flags are documented at https://github.com/iobis/obis-qc.
| Flag | Dropped | Records | |
|---|---|---|---|
| NO_DEPTH | 1,246 |
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| ON_LAND | 648 |
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| NO_MATCH | 215 |
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| NO_ACCEPTED_NAME | 49 |
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| MARINE_UNSURE | 25 |
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| WORMS_ANNOTATION_UNRESOLVABLE | 19 |
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| WORMS_ANNOTATION_REJECT_AMBIGUOUS | 3 |
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| NOT_MARINE | 1 |
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| WORMS_ANNOTATION_RESOLVABLE | 1 |
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