Comparative analysis of Presence-Absence gene Variations in five hard tick species: impact and functional considerations
Additional datasets supporting the "Comparative analysis of Presence-Absence gene Variations in five hard tick species: impact and functional considerations" paper. ABSTRACT Tick species are vectors of harmful human and animal diseases and their expansion is raising concerns under the global environmental changes scenario. Ticks host and transmit bacteria and viruses making the understanding of host-pathogen molecular pathways critical to develop effective disease control strategies. Despite the considerable sizes and repeat contents of tick genomes, individual tick genomics is perhaps the most effective approach to reveal genotypic traits of interest. Presence-Absence gene Variations (PAVs) can contribute to individual differences within species, defining dispensable genes carried by subset of individuals only, possibly underpinning functional significance at individual or population-levels. We exploited 348 350 resequencing datasets of individual Dermacentor silvarum, Haemaphysalis longicornis, Ixodes persulcatus, Rhipicephalus microplus and Rhipicephalus sanguineus hard-tick specimens to reveal the extension of PAV and patterns of dispensable genes among individuals and, comparatively, between species. As resultCompared to the reference genomes, we traced 550-3,346 dispensable genes per species. We complemented the analysis by reconstructing the de-novo pangenome for these five tick species, resulting in 5.3-7 Mb of genomic regions not included in the respective reference genomes. Both the dispensable genes and the de-novo predicted genes mostly referred to transposable elements, indicating that PAV preferentially impacted mobile genetic elements in all these tick species.