DNA barcoding and molecular identification of field-collected Culicoides larvae in the Niayes area of Senegal
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Authors
Bakhoum, Mame Thierno
Sarr, Mamadou
Fall, Assane Gueye
Huber, Karine
Fall, Moussa
Sembene, Mbacke
Seck, Momar Talla
Labuschagne, Karien
Gardes, Laetitia
Ciss, Mamadou
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Publisher
BioMed Central
Abstract
BACKGROUND : Biting midge species of the genus Culicoides Latreille (Diptera: Ceratopogonidae) comprise more than
1300 species distributed worldwide. Several species of Culicoides are vectors of various viruses that can affect
animals, like the African horse sickness virus (AHSV), known to be endemic in sub-Saharan Africa. The ecological and
veterinary interest of Culicoides emphasizes the need for rapid and reliable identification of vector species. However,
morphology-based identification has limitations and warrants integration of molecular data. DNA barcoding based
on the mitochondrial gene cytochrome c oxidase subunit 1 (cox1) is used as a rapid and authentic tool for species
identification in a wide variety of animal taxa across the globe. In this study, our objectives were as follows: (i)
establish a reference DNA barcode for Afrotropical Culicoides species; (ii) assess the accuracy of cox1 in identifying
Afrotropical Culicoides species; and (iii) test the applicability of DNA barcoding for species identification on a large
number of samples of Culicoides larvae from the Niayes area of Senegal, West Africa.
RESULTS : A database of 230 cox1 sequences belonging to 42 Afrotropical Culicoides species was found to be reliable
for species-level assignments, which enabled us to identify cox1 sequences of Culicoides larvae from the Niayes area
of Senegal. Of the 933 cox1 sequences of Culicoides larvae analyzed, 906 were correctly identified by their barcode
sequences corresponding to eight species of Culicoides. A total of 1131 cox1 sequences of adult and larval Culicoides
were analyzed, and a hierarchical increase in mean divergence was observed according to two taxonomic levels:
within species (mean = 1.92%, SE = 0.00), and within genus (mean = 17.82%, SE = 0.00).
CONCLUSIONS : Our study proves the efficiency of DNA barcoding for studying Culicoides larval diversity in field samples.
Such a diagnostic tool offers great opportunities for investigating Culicoides immature stages ecology and biology, a
prerequisite for the implementation of eco-epidemiological studies to better control AHSV in the Niayes region of
Senegal, and more generally in sub-Saharan Africa.
Description
Additional file 1: Figure S1. The minimum cumulative error of false
positive and false negative identifications show the optimum threshold;
for our DNA reference libraries this was around 4.3 and 4.4%, respectively.
Additional file 2: Figure S2. Line plot of the barcode gap for our DNA reference libraries. For each individual in the dataset, the light sky-blue lines represent the maximum intraspecific distance (bottom of line value), and the minimum interspecific distance (top of line value). The red lines show where this relationship is reversed, and the closest non-conspecific is actually closer to the query than its nearest conspecific, i.e. the situation where there is no barcoding gap.
Additional file 3: Table S1. Details of 1131 cox1 sequences representing 40 Afrotropical Culicoides species submitted to BOLD database under the project code “AFCUL”.
Additional file 4: Table S2. Comparison between DNA sequences for Afrotropical Culicoides species using the Barcode Gap Analysis tools on BOLD.
Additional file 2: Figure S2. Line plot of the barcode gap for our DNA reference libraries. For each individual in the dataset, the light sky-blue lines represent the maximum intraspecific distance (bottom of line value), and the minimum interspecific distance (top of line value). The red lines show where this relationship is reversed, and the closest non-conspecific is actually closer to the query than its nearest conspecific, i.e. the situation where there is no barcoding gap.
Additional file 3: Table S1. Details of 1131 cox1 sequences representing 40 Afrotropical Culicoides species submitted to BOLD database under the project code “AFCUL”.
Additional file 4: Table S2. Comparison between DNA sequences for Afrotropical Culicoides species using the Barcode Gap Analysis tools on BOLD.
Keywords
Culicoides, Barcoding, Afrotropical, Senegal, African horse sickness virus (AHSV)
Sustainable Development Goals
Citation
Bakhoum, M.T., Sarr, M., Fall, A.G. et al. 2018, 'DNA barcoding and molecular identification
of field-collected Culicoides larvae in the
Niayes area of Senegal', Parasites and Vectors, vol. 11, art. 615, pp. 1-10.