Abstract:

This dataset contains identification with metabarcoding of fish eggs collected aboard the R/V Hogarth from 2019-08-06 to 2019-09-26 on the West Florida Shelf. This data set includes egg identifications, cruise data, egg picking data, and a sequence ASV table. Dataset associated with the publication: Breitbart M, Kerr M, Schram MJ, Williams I, Koziol G, Peebles E, Stallings CD. 2023. Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf. PeerJ 11:e15016 https://doi.org/10.7717/peerj.15016

Suggested Citation:

Kerr, Makenzie, Grace Koziol, Ernst B. Peebles, Chris Stallings, and Mya Breitbart. 2023. Identification with metabarcoding of fish eggs collected aboard the R/V Hogarth from 2019-08-06 to 2019-09-26 on the west Florida shelf. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/7pvp5zc1

Publications:

Breitbart, M., Kerr, M., Schram, M. J., Williams, I., Koziol, G., Peebles, E., & Stallings, C. D. (2023). Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf. PeerJ, 11, e15016. Portico. https://doi.org/10.7717/peerj.15016

Purpose:

To identify fish spawning sites using metabarcoding collected along the west Florida shelf.

Data Parameters and Units:

Cruise Data Tab: Station ID, Date (MM/DD/YYY); Time on Station EST (hh:mm); Max Station Depth (m); Time Net in EST (hh:mm); Start Latitude (decimal degrees); Start Longitude (decimal degrees); Salinity; Temp; Time Net Out EST (hh:mm); End Latitude (decimal degrees); End Longitude (decimal degrees); Notes Summary Tab: Station Number; Common Name; Total Reads; Percent of Sample Egg Count Data Tab; Picker’s Name (first last); Sample ID; Starting Volume (ml); Ending Volume (ml); Volume Picked (ml); Amount of Alliquots; Number of Eggs Removed; Number of Eggs in Remainder of Sample; Total Number of Eggs in Sample; Date (MM/DD/YYY); Comments Test Sequencing Tab: Species Name (Scientific); NCBI Blast; Percent ID; Sequence

Methods:

Planktonic fish eggs were collected by the R/V Hogarth on two cruises (August 6-16, 2019 and September 24-26, 2019) using a bongo plankton net. Eggs were picked under a dark field dissecting microscope. All eggs from each site were processed together using the Hotshot method mentioned, in Kerr et al. 2020. Metabarcoding was completed using next-generation Illumina sequencing on a small portion of the COI gene. The Divisive Amplicon Denoising Algorithm (DADA2) v1.12 package (Callahan et al. 2016) in R studio was used to process the raw sequence data and obtain filtered and trimmed amplicon sequence variants (ASV). Identification were made using the Barcode of Life Database (BOLD; http://www.boldsystems.org/) and National Center for Biotechnology Information (NCBI Database; https://blast.ncbi.nlm.nih.gov/Blast.cgi).

Provenance and Historical References:

Kerr, M, Browning, J, Bønnelycke, E-M, et al. DNA barcoding of fish eggs collected off northwestern Cuba and across the Florida Straits demonstrates egg transport by mesoscale eddies. Fish Oceanogr. 29: 340– 348. (2020). DOI: 10.1111/fog.12475 Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016). DOI: 10.1038/nmeth.3869

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