The puzzle of DNA sequences of Phytoseiidae (Acari : Mesostigmata) in the public GenBank database
Marie-Stéphane Tixier A B , Fabio Akashi Hernandes A , Sabine Guichou A and Serge Kreiter A
+ Author Affiliations
- Author Affiliations
A Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez, France.
B Corresponding author. Email: tixier@supagro.inra.fr
Invertebrate Systematics 25(5) 389-406 https://doi.org/10.1071/IS11013
Submitted: 3 April 2011 Accepted: 7 July 2011 Published: 14 February 2012
Abstract
The public database GenBank is an increasingly important source of sequence data for diagnostic and phylogenetic research; however, not all deposited sequences are necessarily correctly ascribed to a source species. We considered the example of the mite family Phytoseiidae to determine how the corresponding sequences could be accurately exploited. Phytoseiidae mites are well known worldwide for their ability to control certain mite and insect pests. The number of molecular approaches, especially for diagnostic purposes, has increased over the past decade, leading to an increase in the number of sequences registered in the GenBank database. The aim of the present paper was to evaluate the validity of the DNA sequences presently assigned to Phytoseiidae species in this database. Three hundred and fifty-one sequences, corresponding to the four most frequently registered DNA fragments (ITS, COI, Cytb and 12S rRNA), were considered. DNA extraction, amplification and sequencing were performed for the fragments 12S rRNA and ITS for Amblyseius andersoni, A. swirskii, Iphiseius degenerans, Euseius ovalis, E. stipulatus, Neoseiulus cucumeris and Typhlodromus pyri, as some identifications were questionable. Numerous problems were evident based on genetic distance analyses of these sequences. First, nomenclatural problems were encountered, preventing the correct identification of the taxa sequenced in one case. Suspected misidentifications were frequent, stressing the importance of voucher specimen availability. For the 12S rRNA fragment, sequences assigned to three Phytoseiidae species were those of their prey (Astigmata), underlining the care that must be taken when manipulating the DNA of such predators (sterile conditions and specific PCR primers). Finally, sequences of two regions of the COI mtDNA were encountered, leading to alignment problems between sequences of a same gene and same species. These results are discussed in relation to responsibilities of authors in terms of taxon identification and the great utility of open access DNA sequence databases, such as GenBank, for improving taxonomic identifications and advancing scientific research.
Additional keywords: 12S rRNA, COI, contaminations, Cytb, ITS, misidentification.
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