identifier	taxonID	type	CVterm	format	language	title	description	additionalInformationURL	UsageTerms	rights	Owner	contributor	creator	bibliographicCitation
038B832DFF809060FF16CB34AE8AADE2.text	038B832DFF809060FF16CB34AE8AADE2.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Dna	<div><p>DNA barcode sequencing</p><p>Each specimen caught was sequenced. Total DNA was extracted using Macherey and Nagel NucleoSpin® Tissue kits following the manufacturer’s instructions on an Eppendorf EpMotion 5075®.</p><p>As the aim of our project was to give access to the partial 12 S ribosomal RNA sequence (i.e, the marker most often used for e DNA studies) and the partial COI gene commonly used for barcoding, a part of the mitochondrial genome (called in this study ‘Mt-1’ for ‘the first part of the mitogenome’ starting from the middle of the 12 S to the tRNA-Ser after the COI gene) was amplified following the protocol established by Hinsinger et al. (2015) using the specific primers 12S-L1091R 5’ AAACTGGGATTAGA- TACCCCACTAT 3’ (Kocher et al., 1989) and MtH7061 5’ GGGTTATGTGGCTGGCTTGAAAC 3’(Hinsinger et al., 2015). The Mt-1 fragment provides the sequence of 12 S gene [around 500 bp] and the complete COI gene. Ampli-</p><p>con libraries (Hinsinger et al., 2015) were then sequenced on an Illumina MiSeq sequencer following the manufacturer’s instructions.</p><p>When the Mt-1 fragment reconstruction was difficult, a fragment of the COI gene was amplified with the specific fish primers TelF1 and TelR1 (Dettaï et al., 2011) and used as a reference.</p><p>Data processing was done in Geneious v.11.1.2 (http:// www.geneious.com, Kearse et al., 2012). To reconstruct the Mt-1 fragment of each individual, we used the mtDNA of the species identified morphologically or of the same genus (personal data or sequences available on GenBank) as a starting reference (i.e., for a Map to reference). For the species that had not been sequenced yet at the time of our project, such as, for example, Bleheratherina pierucciae Aarn and Ivantsoff, 2009, a piece of the COI gene was obtained by Sanger sequencing and then used as a starting reference. The consensus of each Mt-1 fragment was primarily checked manually (assembly success, coverage assessment, comparison to available COI sequences for the same specimen, BLAST searches; Altschul et al., 1997). Then the consensus sequence was annotated using MitoAnnotator (Iwasaki et al., 2013) and each gene was checked for coding sequences, stop codons, position of the SNPs.</p></div>	https://treatment.plazi.org/id/038B832DFF809060FF16CB34AE8AADE2	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Mennesson, Marion I.;Charpin, Nicolas;Keith, Philippe	Mennesson, Marion I., Charpin, Nicolas, Keith, Philippe (2024): Fish conservation: importance of DNA reference library based on accurately identified specimens. The case of New Caledonian freshwater fish. Cybium 48 (3): 187-193, DOI: 10.26028/cybium/2024-014, URL: http://dx.doi.org/10.5281/zenodo.14681635
