Assessment of four DNA fragments (COI, 16S rDNA, ITS2, 12S rDNA) for species identification of the Ixodida (Acari: Ixodida)

Abstract

BackgroundThe 5’ region of cytochrome oxidase I (COI) is the standard marker for DNA barcoding. However, COI has proved to be of limited use in identifying some species, and for some taxa, the coding sequence is not efficiently amplified by PCR. These deficiencies lead to uncertainty as to whether COI is the most suitable barcoding fragment for species identification of ticks.MethodsIn this study, we directly compared the relative effectiveness of COI, 16S ribosomal DNA (rDNA), nuclear ribosomal internal transcribed spacer 2 (ITS2) and 12S rDNA for tick species identification. A total of 307 sequences from 84 specimens representing eight tick species were acquired by PCR. Besides the 1,834 published sequences of 189 tick species from GenBank and the Barcode of Life Database, 430 unpublished sequences representing 59 tick species were also successfully screened by Bayesian analyses. Thereafter, the performance of the four DNA markers to identify tick species was evaluated by identification success rates given by these markers using nearest neighbour (NN), BLASTn, liberal tree-based or liberal tree-based (+threshold) methods.ResultsGenetic divergence analyses showed that the intra-specific divergence of each marker was much lower than the inter-specific divergence. Our results indicated that the rates of correct sequence identification for all four markers (COI, 16S rDNA, ITS2, 12S rDNA) were very high (> 96%) when using the NN methodology. We also found that COI was not significantly better than the other markers in terms of its rate of correct sequence identification. Overall, BLASTn and NN methods produced higher rates of correct species identification than that produced by the liberal tree-based methods (+threshold or otherwise).ConclusionsAs the standard DNA barcode, COI should be the first choice for tick species identification, while 16S rDNA, ITS2, and 12S rDNA could be used when COI does not produce reliable results. Besides, NN and BLASTn are efficient methods for species identification of ticks.

New insights from molecular characterization of the tick Rhipicephalus (Boophilus) microplus in Brazil

“…This study sought to obtain high support for the topology of tree and the COX-I molecular marker was found to have the advantage of presenting greater mutation rates than the nuclear marker, corroborating the data presented by Lv et al (2014). However, the ITS-2 molecular marker failed to resolve discrepancies between the populations of R.…”

Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)

“…Single locus data are widely and conveniently used to estimate species boundaries in large samples of specimens of morphology-based taxa (Nicolas et al 2012;Lv et al 2014;Trebitz et al 2015). We tried to disentangle the mitochondrial diversity of the highly variable L. hoffmeisteri, by examining specimens from all continents of the northern hemisphere with ABGD and bGMYC.…”

Comparación y utilidad de las regiones mitocondriales de los genes 16S y COX1 para los análisis genéticos en garrapatas (Acari: Ixodidae)

“…Entre los ejemplos más notables de ajustes taxonómicos en los que los análisis genéticos han sido definitivos en la descripción de nuevas especies y en la identificación de complejos en las familias Ixodidae y Argasidae, están el complejo Rhipicephalus sanguineus (6)(7)(8), el grupo Ornithodoros talaje (9) y el complejo Amblyomma cajennense (10,11). Debido a las peculiaridades biológicas y ecológicas que presentan las diferentes especies y grupos de especies de garrapatas, los estudios genéticos se han convertido en una herramienta importante para explorar las relaciones poblaciones (8,(12)(13)(14), delimitar las especies (15)(16)(17), hacer los análisis filogenéticos (18)(19)(20), e, incluso, identificar potenciales zonas de riesgo de transmisión de enfermedades (3,7,8).…”

“…Entre dichos marcadores se encuentran las secuencias mitocondriales de la subunidad 16S del ARN ribosómico (16S), la subunidad 12S del ARN ribosomal (12S), la región D-loop, el gen de la citocromo oxidasa I (COX1), el gen de la citocromo oxidasa II (COX2), la subunidad 5 de la deshidrogenasa de NADH (NAD5) y regiones nucleares como el espaciador interno transcrito 2 (ITS2), el gen 18S ribosómico, el gen de la subunidad grande ribosómica (LSU), el gen de la ARN polimerasa II (RNApol II) y el gen de la gliceraldehído-3-fosfato deshidrogenasa (G3PDH) (10,(14)(15)(16)(17)(18)20,(21)(22)(23)(24)(25)(26).…”