DOI: 10.23708/53z7fq
title: Alignment of Diaphus spp. nucleotide sequences together with molecular diagnoses of species

description: The dataset contains three files in text format that together provide molecular diagnoses for 60 operational taxonomic units (OTUs) identified in the lanternfish genus Diaphus. METHODS Briefly, Diaphus spp. specimens were captured by pelagic trawling during cruises ESSCHA, NECTAlis, PUFFAlis and WALLAlis of R.V. Alis in the eastern Coral Sea, the Fiji Basin, and the Pacific ocean around Wallis-and-Futuna Islands, sorted on board, and subsampled for genetic analysis. Individual DNA extracts were subjected to PCR amplification of a portion of the CO1 gene using universal CO1 primers for fishes. Partial CO1 gene sequences were produced from PCR amplicons using the Sanger nucleotide sequencing method. A nucleotide sequence dataset was collated, which comprised sequences available from the GenBank and BOLD databases , together with new sequences produced in the course of this survey and deposited in GenBank. Sequences were aligned using the MAFFT algorithm (Katoh et al. 2019) implemented in Geneious v. 7.1.9 (Kearse et al. 2012). OTUs were defined as sequence clusters that form diagnosable molecular lineages or “species” using four distinct algorithms. Details are given in Millet et al. (2022). A number was assigned to each OTU, starting from no. 01 up to no. 60. We used Fedosov et al.’s (2019) MOLD algorithm (v. 20-07, communicated to us by A. Fedosov) to identify nucleotides or combinations of nucleotides diagnostic of an OTU within a large nucleotide-sequence dataset. DESCRIPTION OF DATASET File 1 contains the alignment of nucleotide sequences of 627 Diaphus spp. individuals over a 652-nucleotide long portion of the CO1 gene, including 429 sequences retrieved from the GenBank (Clark et al. 2016) and BOLD (Ratnasingham and Hebert 2007) public databases and 198 new sequences from the tropical southwestern Pacific province sampled through cruises ESSCHA, NECTAlis, PUFFAlis and WALLAlis of R.V. Alis. Sequence labels were constructed as following. For sequences that were retrieved from public sequence databases: GenBank accession no. when available, followed by BOLD no. when available, followed by species name when available, followed by OTU number. For the 198 new sequences that were produced through the present study: oceanographic cruise abbreviation, followed by station no., followed by trawling trait no., followed by specimen no., followed by OTU number. File 2 contains the parameter settings used in the MOLD analysis. File 3 contains the output from MOLD analysis. To navigate through the idiosyncracies of MOLD and to interpret results, see Fedosov et al. (2022). REFERENCES Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016). GenBank. Nucleic Acids Research 44, D67–D72. doi:10.1093/nar/gkv1276. Fedosov A., Achaz G., Puillandre N. (2019) Revisiting use of DNA characters in taxonomy with MOLD ‐ a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets. bioRxiv, https://doi.org/10.1101/838151. Fedosov A.E., Achaz G., Gontchar A., Puillandre N. (2022) MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Molecular Ecology Resources, https://doi.org/10.1111/1755‐0998.13590. Katoh K., Rozewicki J., Yamada K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20, 1160-1166. https://doi: 10.1093/bib/bbx108. Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199. Millet L., Lagrange D., Borsa P. (2022) Species delimitation algorithms applied to a large CO1 barcode dataset of lanternfish Diaphus spp. Institut de recherche pour le développement, Nouméa, 5 p. https://hal.ird.fr/ird-03634906 . Ratnasingham, S., & Hebert, P. D. (2007). BOLD: the barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes 7, 355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.x.