DOI: 10.5281/zenodo.16839899
title: Marine Sponges as Natural Samplers: Advancing integrative strategies for benthic biodiversity assessments

description: 1. Morphology Table Metadata

 


File
Morphology_Table.csv


Creator
Paul Dreger


Date
January - February 2025


Method
Light microscopy


Variables
Sites: Location names          


 
Island: Island on which site is located


 
Date: Month of sampling


 
Labels: Abbreviations for location names


 
Sample_ID: Unique sample ID


 
Volume: Sponge volume


Abstract
This file contains raw counts for all taxa identified by morphological analysis per sample. Associated metadata is given in the form of location details, time of sampling, sample identifiers and sponge volumes used for standardization


Key words
morphology, count, total


File type
CSV, UTF-8 encoding


License
CC BY-NC


Publication
This study




2. OTU Table Metadata

 


File
OTU_Table.csv


Creator
Paul Dreger


Date
Apr 25


Sequencer
MinION Mk1B, R10.4.1. flow cell technology - Oxford Nanopore Technologies


Software
decona v1.4, R 4.4.2


Variables
Barcode: Sample identifier used for tracking samples during metabarcoding


 
uniqueID: Unique sequence ID using Barcode and SeqID


 
SeqID: Identifier of the query sequence used in the BLAST search


 
SseqID: Subject sequence identifier returned by BLAST


 
Total_readcount: Total number of reads associated with the sample/barcode


 
PercIdent: Percentage of identical bases between query and subject sequences


 
Alignmentlength: Length of the alignment between the query and subject sequences


 
Mismatch: Number of mismatched bases in the alignment


 
Gapopen: Number of gap openings in the alignment


 
QueryStart: Starting position of the alignment in the query sequence


 
QueryEnd: Ending position of the alignment in the query sequence


 
SubjectStart: Starting position of the alignment in the reference sequence


 
SubjectEnd: Ending position of the alignment in the reference sequence


 
 Evalue: Expectation value; indicates the number of hits expected by chance


 
Bitscore: Score indicating the quality/significance of the alignment


 
Querylength: Total length of the query sequence


 
Subjectlength: Total length of the reference sequence


 
OTU: Operational Taxonomic Unit assigned based on sequence similarity


 
TaxID: Taxon ID from BOLD/NCBI database


 
Read_Count: Number of reads associated with the OUT


 
domain: Domain name of highest ranking BLAST hit


 
phylum: Phylum name of highest ranking BLAST hit


 
class: Class name of highest ranking BLAST hit


 
order: Order name of highest ranking BLAST hit


 
family: Family name of highest ranking BLAST hit


 
genus: Genus name of highest ranking BLAST hit


 
species: Species name of highest ranking BLAST hit


 
warning: Indicates whether sequence has been assigned to do different taxa with the same likelihood


 
Sequence: Full consensus sequence after reclustering


 
Primer: Primer used to inhibit host DNA amplification (G08R/G3F/None)


 
SampleID: Unique sample ID


 
Island: Island on which site is located


 
Site: Location name


 
Sample_or_Control: Label if sample is a true sample or control


 
quant_reading: DNA quantity of PCR product used in sequencing (ng/µl)


Abstract
This file is the OTU table generated by decona v1.4 from raw FASTQ files (for full command and parameters, see manuscript) containing each consensus sequence with its highest scoring BLAST hit based on E-Value, Percentage Identity and Alignment length. Taxonomic assignment was done using an adjusted version of the "Taxonomy assign  after decona.R" script provided on https://github.com/karlijn-doorenspleet/decona-postprocessing. Raw FASTQ files as well as scripts used for assignment and downstream analyses will be made available in online nucleotide databases (which is to be determined) and GitHub, respectively.


Key words
metabarcoding, otus, blast, taxonomy


File type
CSV, UTF-8 encoding


License
CC BY-NC


Publication
This study