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Background  Calreticulin proteins (CRTs) are important components of tick saliva, which is involved in the blood meal success, pathogen transmission and host allergic responses. The characterization of the genes encoding for salivary proteins, such as CRTs, is pivotal to understand the mechanisms of tick-host interaction during blood meal and to develop tick control strategies based on their inhibition. In hard ticks,  crt  genes were shown to have only one intron with conserved position among species. In this study we investigated the exon-intron structure and variation of the  crt  gene in  Rhipicephalus  spp. ticks in order to assess the  crt  exon-intron structure and the potential utility of  crt  gene as a molecular marker.    Methods  We sequenced the exon-intron region of  crt  gene in ticks belonging to so-called tropical and temperate lineages of  Rhipicephalus sanguineus  ( sensu lato ),  Rhipicephalus  sp. I,  Rhipicephalus  sp. III,  Rhipicephalus  sp. IV,  R. guilhoni ,  R. muhsamae  and  R. turanicus . Genetic divergence and phylogenetic relationships between the sequences obtained were estimated.    Results  All individuals belonging to the tropical lineage of  R. sanguineus  ( s.l. ),  R. guilhoni ,  R. muhsamae ,  R. turanicus ,  Rhipicephalus  sp. III and  Rhipicephalus  sp. IV analysed showed  crt  intron-present alleles. However, both  crt  intron-present and intron-absent alleles were found in  Rhipicephalus  sp. I and the temperate lineage of  R. sanguineus  ( s.l. ), showing the occurrence of an intraspecific intron presence-absence polymorphism. Phylogenetic relationships among the  crt  intron-present sequences showed distinct lineages for all taxa, with the tropical and temperate lineages of  R. sanguineus  ( s.l. ) being more closely related to each other.    Conclusions  We expanded previous studies about the characterization of  crt  gene in hard ticks. Our results highlighted a previously overlooked variation in the  crt  structure among  Rhipicephalus  spp., and among hard ticks in general. Notably, the intron presence/absence polymorphism observed herein can be a candidate study-system to investigate the early stages of intron gain/loss before fixation at species level and some debated questions about intron evolution. Finally, the sequence variation observed supports the suitability of the  crt  gene for molecular recognition of  Rhipicephalus  spp. and for phylogenetic studies in association with other markers.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1909-3) contains supplementary material, which is available to authorized users.

Exon-intron structure and sequence variation of the calreticulin gene among Rhipicephalus sanguineus group ticks