DNA barcoding and surveillance sampling strategies for Culicoides biting midges (Diptera: Ceratopogonidae) in southern India

Abstract

BackgroundCulicoides spp. biting midges transmit bluetongue virus (BTV), the aetiological agent of bluetongue (BT), an economically important disease of ruminants. In southern India, hyperendemic outbreaks of BT exert high cost to subsistence farmers in the region, impacting on sheep production. Effective Culicoides spp. monitoring methods coupled with accurate species identification can accelerate responses for minimising BT outbreaks. Here, we assessed the utility of sampling methods and DNA barcoding for detection and identification of Culicoides spp. in southern India, in order to provide an informed basis for future monitoring of their populations in the region.MethodsCulicoides spp. collected from Tamil Nadu and Karnataka were used to construct a framework for future morphological identification in surveillance, based on sequence comparison of the DNA barcode region of the mitochondrial cytochrome c oxidase I (COI) gene and achieving quality standards defined by the Barcode of Life initiative. Pairwise catches of Culicoides spp. were compared in diversity and abundance between green (570 nm) and ultraviolet (UV) (390 nm) light emitting diode (LED) suction traps at a single site in Chennai, Tamil Nadu over 20 nights of sampling in November 2013.ResultsDNA barcode sequences of Culicoides spp. were mostly congruent both with existing DNA barcode data from other countries and with morphological identification of major vector species. However, sequence differences symptomatic of cryptic species diversity were present in some groups which require further investigation. While the diversity of species collected by the UV LED Center for Disease Control (CDC) trap did not significantly vary from that collected by the green LED CDC trap, the UV CDC significantly outperformed the green LED CDC trap with regard to the number of Culicoides individuals collected.ConclusionsMorphological identification of the majority of potential vector species of Culicoides spp. samples within southern India appears relatively robust; however, potential cryptic species diversity was present in some groups requiring further investigation. The UV LED CDC trap is recommended for surveillance of Culicoides in southern India.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1722-z) contains supplementary material, which is available to authorized users.

Phylogenetic relationships and molecular delimitation of CulicoidesLatreille (Diptera: Ceratopogonidae) species in the Afrotropical region: interest for the subgenus Avaritia

“…In our study, phylogenetic relationships and molecular delimitation of species using bPTP on the concatenated phylogenetic tree were in accord with that delimited by morphology, but less so with bGMYC based on COI , 16S rDNA and 28S rDNA genes, and showed potential cryptic species within the clusters of C. bolitinos , C. pseudopallidipennis and C. oxystoma . In fact, Cornet and Brunhes suggested that C. oxystoma is a species complex (Cornet & Brunhes, ); this is corroborated by the highest level of intraspecific divergence being observed in C. oxystoma based on COI sequences in previous studies (Bakhoum et al ., ; Harrup et al ., ). In our opinion, further investigation of C. oxystoma specimens from the distribution area of this species (West Africa, Saharo‐Arabian, Oriental and Australian regions) is necessary in order to delineate species within the Oxystoma group.…”

“…This subgenus, with C. schultzei as type species, includes the Schultzei group with species of veterinary interest, such as C. kingi involved in the transmission of Onchocerca gutturosa , a widespread parasite of Sudanese cattle (El Sinnary & Hussein, ) or C. oxystoma , potential vector of Akabane virus in Japan (Kurogi et al ., ) and AHSV in Senegal (Fall et al ., ; Bakhoum et al ., ). Molecular delineation using bPTP and bGMYC methods for C. oxystoma from Lebanon and Senegal showed that C. oxystoma is a complex of sibling species, as previously noted by several authors (Cornet & Brunhes, ; Bakhoum et al ., ; Harrup et al ., ). In order to examine potential species within C. oxystoma , we suggest the use of Bayesian species delimitation implemented in Bayesian Phylogenetics and Phylogeography (BPP) (Rannala & Yang, ; Yang & Rannala, ) in future investigations.…”

“…The following sequences were used in this study: COI sequences from a C. bolitinos Meiswinkel population from Reunion Island (A. Desvars, J.C. Delecolle, F. Biteau, G. Gerbier, F. Roger and T. Baldet, unpublished data) [accession numbers: HQ447061.1 and HQ447062.1], a C. fulvus Sen and Das Gupta population from Australasia (Gopurenko et al ., ) [accession numbers: KT352267.1, KT352340.1, KT352547.1, KT352629.1 and KT352696.1], a C. miombo Meiswinkel population from Benin (B. Mathieu, C. Garros, T. Balenghien, E. Candolfi, J.C. Delecolle, and C. Cetre‐Sossah, unpublished data) [accession numbers: KF417704.1 and KF417705.1] and a C. similis Carter population from India (Harrup et al ., ) [accession numbers: KT307841.1‐KT307842.1]; and CAD sequences from C. kwagga , C. loxodontis Meiswinkel, C. gulbenkiani Caeiro, C. tuttifrutti Meiswinkel and C. bolitinos populations from South Africa [accession numbers: KJ163032.1, KJ163034.1, KJ163025.1, KJ163044.1, KJ163009.1], and C. imicola Kieffer from France [accession number: KJ163028.1] (Bellis et al ., ).…”

Blood-feeding, susceptibility to infection with Schmallenberg virus and phylogenetics of Culicoides (Diptera: Ceratopogonidae) from the United Kingdom

“…The phylogenetic relationships among taxa were resolved using a Bayesian inference (BI) approach using the HKY+G nucleotide substitution model rooted on the partial cox1 sequence of C. imicola Kieffer (GenBank: KT307824) [48]. The BI tree was constructed using MrBayes v. 3.2.2 [46,49] and twenty million tree generations in four chains were run, sampling every 1000th and discarding the first 25%, before constructing a 50% majority rule consensus tree reporting Bayesian posterior probabilities.…”

The State of Phylogenetic Analysis: Narrow Visions and Simple Answers—Examples from the Diptera (flies)

“…One difficulty as presented by some studies where CO1 sequencing and, perhaps, that of another gene or two is used as a phylogenetic tool is that they often concern relatively small groups of morphologically similar species such as species groups of Culicoides (Ander et al, 2013;Bakhoum et al, 2013;Bellis et al, 2014;Harrup et al, 2016;Muñoz-Muñoz et al, 2014;Pagès et al, 2009;Sarvašová, et al, 2017;Talavera et al, 2017;Tay et al, 2016). Morphologically-based synapomorphies are less likely to be evident (or present) in such similar species groups.…”