A study of the composition of the Obsoletus complex and genetic diversity of Culicoides obsoletus populations in Spain

Background The Culicoides obsoletus species complex (henceforth ‘Obsoletus complex’) is implicated in the transmission of several arboviruses that can cause severe disease in livestock, such as bluetongue, African horse sickness, epizootic hemorrhagic disease and Schmallenberg disease. Thus, this study aimed to increase our knowledge of the composition and genetic diversity of the Obsoletus complex by partial sequencing of the cytochrome c oxidase I (cox1) gene in poorly studied areas of Spain. Methods A study of C. obsoletus populations was carried out using a single-tube multiplex polymerase chain reaction (PCR) assay that was designed to differentiate the Obsoletus complex sibling species Culicoides obsoletus and Culicoides scoticus, based on the partial amplification of the cox1 gene, as well as cox1 georeferenced sequences from Spain available at GenBank. We sampled 117 insects of the Obsoletus complex from six locations and used a total of 238 sequences of C. obsoletus (ss) individuals (sampled here, and from GenBank) from 14 sites in mainland Spain, the Balearic Islands and the Canary Islands for genetic diversity and phylogenetic analyses. Results We identified 90 C. obsoletus (ss), 19 Culicoides scoticus and five Culicoides montanus midges from the six collection sites sampled, and found that the genetic diversity of C. obsoletus (ss) were higher in mainland Spain than in the Canary Islands. The multiplex PCR had limitations in terms of specificity, and no cryptic species within the Obsoletus complex were identified. Conclusions Within the Obsoletus complex, C. obsoletus (ss) was the predominant species in the analyzed sites of mainland Spain. Information about the species composition of the Obsoletus complex could be of relevance for future epidemiological studies when specific aspects of the vector competence and capacity of each species have been identified. Our results indicate that the intraspecific divergence is higher in C. obsoletus (ss) northern populations, and demonstrate the isolation of C. obsoletus (ss) populations of the Canary Islands. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04841-z.

Culicoides imicola, a member of the subgenus Avaritia, is deemed the major BTV, AHSV and EHDV vector in Africa, the Middle East, southeast Asia and southern Europe [5,12]. C. imicola is highly abundant in central and southern regions of mainland Spain [13,14]. Carpenter et al. [15] showed the vector competence of several Palearctic species of Culicoides prior to the introduction of BTV-8 into northern Europe. After the BTV-8 epizootic in northern Europe, several species of different subgenera were implicated as potential competent BTV vectors in the field: Culicoides chiopterus [16], Culicoides dewulfi, and the Culicoides obsoletus species complex (henceforth 'Obsoletus complex') of the subgenus Avaritia [17]; and the Culicoides pulicaris species complex (henceforth 'Pulicaris complex') [17] of the subgenus Culicoides. In areas of northern European, the Obsoletus complex is considered of great importance in BTV transmission due to its predominance and prevalence in entomological surveys [18], and its vector competence [15,19,20]. The Obsoletus complex is widespread in Spain, although it is most abundant in northern regions of the country [13,14]. Moreover, C. obsoletus breeds in diverse habitats with high organic content, including livestock manure [21][22][23], and it can breed in indoor locations [24], which implies a great risk of BTV transmission to livestock.
Females of the species that belong to the Obsoletus complex (C. obsoletus and C. scoticus and cryptic species/ clades within the complex) are difficult to distinguish morphologically [25,26]. Thus, many studies aimed at assessing oral susceptibility to BTV and EHDV in these sibling species have been performed at the species complex level [15,20,27]. Other studies have studied vector competence at species level within the complex, but with a low number of insects [19,28]. Those studies proved the susceptibility of the Obsoletus complex to different BTV serotypes [15,19,20,28], and one EHDV serotype [27]. To our knowledge, no study has been carried out on the oral susceptibility of the Obsoletus complex to AHSV, but one study achieved the isolation of AHSV from pools consisting mainly of the Obsoletus and Pulicaris complexes during the 1987-1989 Spanish epizootic [29]. However, sibling species within the complex may have different vector competence and capacities [30].
The mitochondrial DNA (mtDNA) cytochrome c oxidase I (cox1) gene is widely used for the molecular identification of species and to study their genetic diversity [31], and is also frequently used to study the diversity of the Obsoletus complex [2,[32][33][34][35][36][37]. Few studies have yielded Obsoletus complex sequences of cox1 in Spain [32][33][34], although a recent study investigated the genetic diversity of the Obsoletus complex at a large scale using insects from 20 different countries, including Spain [35]. The majority of available Spanish cox1 Obsoletus complex sequences have come from Catalonia and the Balearic Islands [33,35], southeastern areas of Spain [35] and the Canary Islands [32]. The importance of the Obsoletus complex as a biological vector of pathogens that cause severe diseases in livestock [1] justifies the aim of this study to expand our knowledge of the composition and genetic diversity of the Obsoletus complex by using the partial sequencing of the cox1 gene in poorly studied areas of Spain, as well as to compare our results with georeferenced sequences from Spain that have been deposited in GenBank [38]. Moreover, we developed a multiplex polymerase chain reaction (PCR) to facilitate the differentiation of C. obsoletus from C. scoticus in the region.

Specimen collection and identification
The 117 insects that were analyzed in the current study originate from mainland Spain (they were provided by the Spanish Bluetongue National Surveillance Program), and from a trap that we placed in the Canary Islands (Table 1). Figure 1 shows the location of the collection sites used in this study and those of the georeferenced sequences retrieved from GenBank (Additional file 1: Table S1) [38]. United States Centers for Disease Control and Prevention ultraviolet light traps were located in all six collection sites at 1.7-to 2-m height from dusk until dawn close to animal holdings with more than ten susceptible hosts [39]. Insects were preserved in 70% ethanol prior to identification, and we analyzed females identified as belonging to the Obsoletus complex using different morphological identification keys [40,41].

DNA extraction and molecular identification
DNA extraction was performed using the High Pure PCR Template Preparation Kit (Roche Diagnostics, Mannheim, Germany) following the manufacturer's instructions. Specimens had previously been removed from ethanol, dried on absorbent paper, and then homogenized in 100 μl of binding buffer.  [42]). Locations are coded based on the province's location (see Table 1 For the partial amplification of the mtDNA cox1 region, we designed two pairs of primers using Prim-er3Plus v.2.4.2. software [43]. For C. obsoletus (ObL), forward (5′-GGR GTA TGA GCC GGA ATA AT-3′) and reverse (5′-ATT TCG RTCDGTT AAR AGYA-3′) primers were designed with a product size of ~ 576 base pairs (bp). For C. scoticus (ScN), we designed forward (5′-TGC TCC CYC CTT CAA TCA CT-3′) and reverse (5′-ATG CCG GTA GAT CGC ATA TT-3′) primers to amplify a shorter sequence (~ 217 bp) of the cox1 region. We checked the sensitivity and specificity of the primer pairs from European C. obsoletus and C. scoticus sequences available in GenBank [38] (https:// www. ncbi. nlm. nih. gov/ genba nk/) (Fig. 2). PCR amplification was performed in a 25-μl final volume using the following reagents per reaction: 2 μl of Nuclease-free water, 15 μl of Platinum Green Hot Start PCR 2X Master Mix (Invitrogen, Lithuania), 1.5 μl of 20 μM forward primers (ObL and ScN), 1.5 μl of 20 μM reverse primers and 2 μl of genomic DNA. The amplification program was as follows: an initial denaturation step at 94 ºC for 5 min, 40 cycles of denaturation at 94 ºC for 1 min, annealing for 1 min and extension at 72 ºC for 1 min, and a final extension step at 72 ºC for 7 min. We optimized the annealing temperature to enhance the specificity to evaluate different annealing temperatures from 54 to 60 ºC in increments of 2 ºC. PCR products were stored at 4 ºC until the amplification of the PCR products was confirmed using electrophoresis on 2% agarose 1x TAE gel that contained SYBR Safe DNA Gel Stain (Invitrogen, USA), with a 100-bp DNA molecular weight marker (Takara). PCR products were purified using QIAquick PCR Purification kit (Qiagen, Germany) in the absence of primer dimer formation. Alternatively, gel bands were purified using QIAquick Gel Extraction kit (Qiagen) and forward strands were externally sequenced by Sanger sequencing using the ObL forward primer. We assigned the Culicoides species level using BLASTN+ 2.10.1 nucleotide [44].

Molecular analysis and phylogenetic tree
For the molecular analyses and intraspecific sequence polymorphism of C. obsoletus (ss), we included cox1 georeferenced sequences from Spain of C. obsoletus, which are available from the GenBank database (https:// www. ncbi. nlm. nih. gov/ genba nk/). DNA polymorphism and haplotype diversity were obtained using DnaSP v.6.12. [45]. A median-joining network for the identified haplotypes was built using Network software v.10.2.0.0 [46], to show the relationships between them. Pairwise genetic differentiation was assessed using the fixation index (F ST ) calculated in DnaSP [45]. F ST -values can range between 0 and 1, where 0 shows no differentiation, and 1 no genetic diversity shared between populations [47].
All phylogenetic analyses were performed in MEGA X [51]. Sequences were aligned using the MUSCLE algorithm [52], and the suitability of the alignment was evaluated through the average evolutionary divergence for all nucleotide sequence pairs (p-distance). To generate a reliable phylogenetic tree, we set the threshold value for the p-distance at < 0.8 [53,54]. We inferred a maximum likelihood (ML) phylogenetic tree with the general time reversible model [55] with a gamma distribution and invariant sites, and using 2000 bootstrap replications for reliability. Tree branches with bootstrap values inferior to 50% were collapsed to form a consensus tree [56].

cox1 multiplex PCR optimization
We evaluated four annealing temperatures in our multiplex cox1 PCR: 54, 56, 58 and 60 ºC. The annealing temperature which improved the specificity was 60 ºC (Fig. 3). For every other temperature, non-specific PCR bands were obtained for C. scoticus samples. Hence, the optimal annealing temperature for maximal specificity was 60 ºC. However, for poor-quality samples, we found that it might be advisable to decrease the annealing temperature in order to increase sensitivity.
For C. scoticus from the Canary Islands site, ObL primers amplified a ~ 576-bp band with an annealing temperature of 54 ºC. These bands were purified and sequenced using the ObL forward primer. Thus, sequences of C. scoticus from that location were obtained and included in further analyses. The amplification of some C. scoticus sequences with an annealing temperature of 54 ºC made it necessary to increase the temperature to 60 ºC to be able to correctly differentiate the species and prevent non-specific PCR bands.

Obsoletus complex sequence diversity for sampled sites
Of the 117 Obsoletus complex individuals studied here, 90 were identified as C. obsoletus (76.92%), 19 as C. scoticus (16.24%) and five as C. montanus (4.27%); three could not be identified (2.56%). The proportion of each species differs greatly in the six sites chosen for the study (Table 1). In SE and AV, all identified insects were C. obsoletus, while in GC1 half of the individuals were C. scoticus. In AS, CS and C, we identified a total of six C. scoticus individuals. C. montanus was identified in CS and C.
We obtained a total of 90 sequences for C. obsoletus, 13 for C. scoticus of the Canary Island location, and five for C. montanus. All 108 sequences had a length of 514 bp. We found 19 haplotypes for C. obsoletus (Ob01-Ob19), three for C. scoticus (Sc01-Sc03) and one for C. montanus. Sequences from each haplotype were deposited in GenBank under the following accession numbers: C. obsoletus (MW602810-MW602828), C. scoticus (MW602829-MW602831), and C. montanus (MW602832). The most prevalent C. obsoletus haplotype was Ob13, which was present at all six sampling sites (Fig. 4), and represented 42.22% (38/90) of all C. obsoletus sequences. The Ob13 haplotype was predominant at GC1 (12/13-92.31%), SE (4/5-80%) and CS (11/22-42.22%). Ob10 was found at the four northern locations, while Ob02 and Ob03 were found in C and AS, Ob05 in AV and CS, and Ob07 and Ob11 in AV and C. Ob08 was only found at C, Ob012 at AV, and Ob04 at AS, but at a relatively high proportion: 5/22 (22.72%), 4/18 (22.22%) and 3/10 (30%), respectively, at each site. The rest of the haplotypes were only found at one site in low numbers. For the C. scoticus population in the GC1 population, 11/13 individuals belonged to haplotype Sc03; in contrast, Sc01 and Sc02 haplotypes were are only represented by one individual.
We found that the interspecific nucleotide divergence was greater than the intraspecific diversity, as previously demonstrated [2,35]. The total nucleotide diversity for all of the sequences was 0.0307 ± 0.0053, while for the C. obsoletus (ss) sequences it was 0.0045 ± 0.0004, and for C. scoticus 0.0006 ± 0.0003. Table 2 shows the sequence polymorphism of C. obsoletus (ss) populations obtained in the present study and from georeferenced sequences retrieved from GenBank.

C. obsoletus sequence diversity compared with external Spanish sequences
We obtained 148 C. obsoletus (ss) georeferenced sequences from Spain from GenBank (Additional file 1: Table S1), and aligned them with our sequences, which gave a total of 238 sequences. The final length of the alignment was 457 bp, and we identified 23 C. obsoletus (ss) haplotypes. Of 148 external sequences, 141 corresponded to one of the haplotypes identified in this study. We maintained the numbering of the identified haplotypes and added consecutive numbers for the new haplotypes identified from the GenBank sequences (Ob20-25). Due to the similarities of the sequences obtained in this study (Additional file 2: Table S2) and their shortening, three pairs of haplotypes had the same sequence in the 457-bp alignment: haplotypes Ob03 and Ob10 (Ob03-Ob10), Ob09 and Ob15 (Ob09-Ob15), as well as Sc01  Table 2 Intraspecific polymorphisms of the sequences of C. obsoletus (ss) populations evaluated in this study and of georeferenced sequences retrieved from GenBank The analysis was performed using a 457-bp alignment h Number of haplotypes, Hd haplotype (gene) diversity, S number of variable sites, π nucleotide diversity (per site) a Identifies the geographical location (see Fig. 1 and Sc03 (Sc01-Sc03). Figure 5 shows haplotype relationships determined using a median-joining network.
Ob13 was the most frequent haplotype, comprising 51.26% (122/238) of the sequences, and was present at all collection sites. Ob03-Ob10, Ob09-Ob15 and Ob05 also occurred at a relatively high frequency, i.e. in ten or more insects. Eleven haplotypes were from only one individual: six of those identified in our samples and five from Gen-Bank georeferenced sequences.
We found more C. obsoletus (ss) haplotypes and genetic diversity at B, C, AV, CO and CS (Table 2). However, SE, AL and the Canary Islands (GC1-3 and TF) populations had significantly lower intraspecific diversity, although few sequences were included for SE and AL. A pronounced level of genetic differentiation was observed between each Canary Island population, mainland Spain and IB populations in this study with F ST values > 0.25, as well as between SE and AS, AV, B and GR (Table 3). Negative F ST values can be a result of a small sample size in relation to a high number of haplotypes in the population, and should be considered as indicating no genetic differences [57]. Thus, no divergence was found among the Canary Island sites, or with SE, or between some populations on mainland Spain.

Phylogenetic analysis
The alignment was suitable for the generation of reliable phylogenetic trees, with an average of 0.09 nucleotide substitutions per site when taking into consideration all sequence pairs. The ML phylogenetic tree (Fig. 6) showed that the sequences analyzed here have a small evolutionary distance; this was also supported by the low nucleotide diversity (Additional file 2: Table S2). The tree also corroborates the absence of cryptic species in the area of study.

Discussion
In the present study, a single-tube multiplex PCR assay based on the partial amplification of the mtDNA cox1 gene was developed. Previous studies have also developed single-tube multiplex PCR assays for the cox1 gene for the Obsoletus complex [37,58,59]. However, the amplicon size for C. obsoletus used in these assays was inadequate for our posterior sequence diversity and phylogeographic analyses. Our PCR allows the differentiation of C. obsoletus from C. scoticus within the Obsoletus complex, without the need for sequencing derived from the use of generic primer pairs such as LCO/HCO [60], C1-J-1718/C1-N-2191 [61,62], and Lep [63], although ObL primers showed a lack of specificity for the amplification of C. montanus, which we discuss below. We found some cross-reactivity with the ObL primers and C. scoticus samples at low annealing temperatures, although we designed the primers so as to avoid this. This crossreactivity was overcome by using an annealing temperature of 60 ºC (Fig. 3). Other authors have pointed out similar difficulties concerning the specificity of specifically designed primers for Culicoides species [48]. We did not evaluate whether our primers could amplify other Culicoides species outside the Obsoletus complex, thus previous morphological identification cannot be substituted by our molecular approach. Moreover, morphological identification of all the midges as belonging to the Obsoletus complex coincided with their molecular identification. The correct morphological identification is key to accurately estimate the large-scale distribution of Culicoides species and complex when molecular identification is not achievable.
Primers designed for C. obsoletus (ObL) also amplified one haplotype of C. montanus. The existence of other cross-reactions cannot be ruled out for other Obsoletus complex species haplotypes that were not identified in this study for Spain, or for other geographical regions. To overcome the limitations regarding specificity that were encountered for C. montanus and some haplotypes of C. scoticus at low annealing temperatures of the applied primers, a multi-marker approach including other mitochondrial (cox2 and cytb) and nuclear loci (ITS1 and ITS2) should be considered for future studies in which the main goal is to correctly differentiate between C. obsoletus (ss), C. scoticus, C. montanus and all cryptic species within C. obsoletus [64]. To our knowledge, no PCR for the cox1 gene that has been designed enables discrimination of C. montanus within the Obsoletus complex/group [37,48,58,59]. Due to the low genetic distance between C. obsoletus (ss) and C. montanus ( Fig. 6; Additional file 2: Table S2) [35], it is highly unlikely that specifically generated primers created for C. obsoletus (ss) do not also amplify C. montanus, especially if the latter species has not been taken into account in the primer design, as our results show. Some authors have been able to correctly differentiate C. montanus from C. obsoletus using the ITS1 [67] and ITS2 markers [66,68], although other studies faced similar specificity limitations to ours when identifying C. montanus in a PCR designed specifically for C. obsoletus that used the ITS2 marker [69].
The prevalence of C. montanus is generally low in entomological surveys, with the exception of some studies carried out in Morocco [35]. Therefore, its role as an arbovirus vector has not yet been defined. In addition, the taxonomic status of C. montanus in western Palearctic regions has been questioned by some authors due to the low genetic distance found between it and C. obsoletus (ss) when using different molecular markers [35,65,66].
We found higher genetic diversity in mainland Spain than in the Canary Islands ( Table 2). The low genetic diversity, inexistent genetic differentiation among the structure of C. obsoletus (ss) in all Canary Islands populations, and strong divergence with the other sampling sites (Tables 2, 3) are probably a consequence of their isolation, which implies inbreeding and low gene flow outside the islands [70]. On the other hand, for site IB there was no to low differentiation with mainland Spain, except for site B with which there was moderate divergence, as it had three of the most prevalent haplotypes in this study: Ob03-Ob10, Ob05 and Ob13 (Fig. 5). Its closeness to mainland Spain may facilitate gene flow between midge populations of the two. Haplotype and nucleotide diversity in the south of mainland Spain is lower than in northern areas of Spain. These differences can be attributed to sample size; however, the abundance of the Obsoletus complex is higher in northern and mountainous areas of Spain [14], and genetic diversity is partially influenced by population size [70]. In addition to differences in population size, orographic barriers such as altitude (Fig. 1), might limit genetic flow between some of the mainland populations in this study, although the limited sample size of some collection sites prevents us from drawing a firm conclusion (Table 3). We found similar overall proportions of each species to those reported in recently published work [35]. In Mignotte et al. [35], of the 179 sequences analyzed for samples from Spain, 128 (71.51%) were from C. obsoletus, two from (1.12%) C. montanus, 28 (15.64%) from C. scoticus and 21 (11.73%) from C. scoticus clade 2, although in a site in Catalonia, only C. scoticus midges were identified. Moreover, there are dissimilar ratios for the Canary Islands between our study and that of Mignotte et al. [35], since we identified a 1:1 ratio for C. obsoletus (ss) and C. scoticus, while in the latter study, C. scoticus was not found. The peculiar orographic characteristics of the Canary Islands justify strengthening our knowledge of the Obsoletus complex composition there, in collection sites that are more homogeneously distributed. We did not find C. scoticus clade 2, although we did not obtain a large sequence for any of the six C. scoticus midges from mainland Spain. Moreover, we did not find evidence of any cryptic species at any of the sampled sites, as in studies carried out in nearby countries, such as Morocco [35,71]. Both C. obsoletus O2 and C. obsoletus clade dark or O3 have been described from Switzerland, Sweden, Denmark, Finland, Latvia, Norway, France and Italy at latitudes above 45º [35,48,50]. The former has also been described from Poland [35], and C. obsoletus clade dark or O3 from the Netherlands [49]. In the United Kingdom, evidence of Obsoletus complex cryptic taxa has also been found [36]. Cryptic species may have significant epidemiological differences in terms of vector competence, host preferences and breeding sites, although there is as yet no evidence for this [30]. Our results, along with those of previous work carried out on Spanish populations of the Obsoletus complex [33][34][35], show that C. obsoletus cryptic species O2 and clade dark might be absent from Spain, present in very low numbers, or present in unsampled locations. The potential absence of cryptic taxa from the Obsoletus complex in Spain may be of relevance to future epidemiological studies, as species-specific vector competence within the complex could be examined by using a greater number of insects [19,28]. Nevertheless, more C. obsoletus sequences should also be acquired to definitively exclude the presence of cryptic species in areas with a high abundance of the Obsoletus complex, namely, northern locations [13,14], which also show more genetic diversity (Table 2).
According to the entomological survey which has been conducted by the Spanish Bluetongue National Surveillance Program since 2004, the Obsoletus complex is the most abundant in northern areas of mainland Spain and the C. imicola complex is generally absent or found in low numbers [14]. Therefore, it is thought that the Obsoletus complex plays a key role in the transmission of BTV there, given that it is a competent vector of the virus [15,19,20]. The persistence of BTV in northern Spain was empirically proven by the circulation of BTV-1 from 2007 to 2009 and BTV-8 in 2008 and 2020 [72]. However, the exact contribution of the Obsoletus complex to BTV transmission in central and southern areas of mainland Spain, where C. imicola is the main vector of BTV, has not yet been well defined [13,73].

Conclusions
Our study reveals that C. obsoletus (ss) is the predominant species within the Obsoletus complex in mainland Spain. This information may be of relevance for future epidemiological studies when more robust information is available on specific aspects of the vector capacity (vector competence, adult longevity, biting rate [1]) of each of the sibling species of this complex. Our results show that intraspecific divergence is higher in C. obsoletus (ss) northern populations, and highlight the isolation of C. obsoletus (ss) populations in the Canary Islands. No cryptic species within C. obsoletus were identified.