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closeCOI sequences of P. miles and P. volitans by Turan et al. (2020)
Posted by C.Turan on 23 Oct 2021 at 09:24 GMT
COI sequences of P. miles and P. volitans individuals collected from the Iskenderun Bay by Turan et al. (2020) were cristisesed in the Discussion section. The COI sequences of P. miles and P. volitans individuals were not deposited to the GenBank-NCBI at that time. As they mentioned, 9 COI haplotypes for P. miles and 7 haplotypes for P. volitans were given in Table 2 of the study (Turan et al., 2020, 81 basepair COI sequence of examined 609 bp COI region). Çınar et al. (2021) mentioned that “the Haplotypes do not match with “any” sequence in the GenBank when searched in NCBI Blast and match various sequences of Bacteria, Yeast, Fungi, Plants, etc. in the GenBank”. This statement indicates that the authors have very poor genetic knowledge. Haplotypes are not subsequent nucleotides of COI; they are composed of variable sides of COI as mentioned in the text of the study (Turan et al. 2020). In Table 2 of the study (Turan et al. 2020), it is mentioned on the left sidebar as haplotypes (Hap_1, Hap_2, …), and at the top of Table 2, “variable nucleotide positions of COI DNA…” which means that the variables nucleotides are distributed along the examined 609 bp COI region. These haplotypes were generated by the used genetic software. It is meaningless and unfortunate to expect these haplotypes to definitely match any complete sequences of Pterois or other fish species. Çinar et al. (2021) also mentioned that “They have neither included any previously published genetic data in their study nor have they deposited their sequences in NCBI or BOLD databases”. This is our choice and it is none of these authors' business. Çinar et al. (2021) also mentioned that “the COI sequences given by Turan et al. (2020) are not related to the COI barcodes for any Pterois species”. As we pronounced above, they are “haplotypes” as given in Table 1 and 2, they are not subsequent nucleotides of COI and, therefore, do not have a chance to match with any complete sequences of Pterois species. We used the term barcode in the explanation of Table 2 to mention that the haplotypes have species-specific features as a barcode to distinguish Pterois species. The authors gen access to the COI sequences of P. miles and P. volitans from GenBank (OK326928-OK326945)
TURAN, C., Ali, U. Y. A. N., GÜRLEK, M., & DOĞDU, S. A. (2020). DNA Barcodes for Identifications of Two Lionfish Species Pterois miles (Bennett, 1828) and Pterois volitans (Linnaeus, 1758) in the Mediterranean. FishTaxa, 16, 29-36.
RE: COI sequences of P. miles and P. volitans by Turan et al. (2020)
myokeş replied to C.Turan on 07 Jun 2022 at 10:10 GMT
As Turan mentioned in his response, depositing the sequences in NCBI or BOLD may be the author’s choice, not “our business”, but it's the scientists' responsibility to criticize the inconsistencies in a scientific study built on samples and gene sequences that no one has access to. In response to Çınar et al. (2021), Turan kindly gave the gene bank accession numbers of the sequences that are the subject of the article in question.
We are grateful that we found chance to analyze data belonging to an alien species which is said to be in the Mediterranean since 2016. However, this may not be also “our business”, but, after all the critisim, it is hard to understand why the authors,16 months later than the publication (Turan et al. 2020), uploaded only the 233 bp 3’ portions of the sequences, instead of 609 bp full length, which said to be analyzed in their study. Nevertheless, we downloaded all of the sequences from GenBank (OK326928-OK326945) as well as other COI sequences deposited in the GenBank by other researchres; for Pterois miles: KR861550 (Lebanon), MT076824 (United Arab Emirates), MT889035 (Mauritius), LK022697 (Israel-Eilat), MF124021 (Israel-Eilat), JF494333 (South Africa); for Pterois volitans: HQ956444 (Australia), KP194970 (Australia), GU673823 (Indonesia), FJ584040 (Vietnam), FJ584042 (Vietnam), HQ966023 (Mexico), JN312282 (Mexico) and KJ739816 (Mexico).
First we aligned the sequences mentioned by Turan (OK326928-OK326945) with ClustalW on MEGAX platform (Kumar et al., 2018), and observed 19 variables sites. But when the conserved positions between the variable sites are deleted, as it is said to be done in Turan et al. (2020), the emerging pattern of varible sites was completely different from the pattern shown in the article. The Pterois miles sequences from Iskenderun aligned perfectly with the 413-645 bp 3’ residue of the Pterois miles sequence from Lebanon. On the other hand, the the Pterois volitans sequences from Iskenderun aligned perfectly with other Pterois volitans sequences retrieved from GenBank. Thus, it is obvious that the indentities of the species entered to GenBank by Turan (OK326928-OK326945) are correct. However, those Pterois volitans sequences are not related to the Pterois volitans sequrences they have examined in their publication (Turan et al., 2020). We aligned all the sequences downloaded from GenBank and find all variable sites between the two species. Unfortunately the pattern of variable sites do not show any similarity with Turan et al. (2020)
Sorry to say that, Turan’s response to clarify the “our misunderstanding” of their work created more inconsistencies, rather than solving the problem. Since the bioinformatic analysis performed on the supporting genetic data provided by Turan gives totally different results when compared to their publication, We believe that the genetic data shown by Turan et al. (2020) have major issues and not dependable. We still believe that we do not have any data to support the presence of Pterois volitans along the coasts of Turkey.