Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing

Abstract

BackgroundGlobal warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I. ricinus tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for I. ricinus ticks and the embryo-derived cell line IRE/CTVM19.Results235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick’s North American relative Ixodes scapularis. After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95–100% identity to the corresponding I. scapularis gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for I. ricinus ticks and 3.80 Gb for the cell line.ConclusionsWe present a first draft sequence map of the I. ricinus genome based on a PacBio-Illumina assembly. The I. ricinus genome was shown to be 26% (500 Mb) larger than the genome of its American relative I. scapularis. Based on the genome size of 2.65 Gb we estimated that we covered about 67% of the non-repetitive sequences. Genome annotation will facilitate screening for specific molecular pathways in I. ricinus cells and provides an overview of characteristics and functions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2008-9) contains supplementary material, which is available to authorized users.

Hard ticks as research resources for vector biology: from genome to whole-body level

“…For the genome sequencing, the I. scapularis colony established in 1996 and maintained at the University of Connecticut Health Center was selected (Hill and Wikel, 2005). In 2016, the genome assembly of I. scapularis, was completed (Gulia-Nuss et al, 2016) and then draft genome assembly was performed for I. ricinus (Linnaeus, 1758) (Charles River strain), the European vector of Lyme disease borreliae and tick-borne encephalitis (TBE) virus (Cramaro et al, 2015(Cramaro et al, , 2017. These medically important Ixodes ticks and I. persulcatus distributed in the Asia-Pacific region are proposed for genome analysis as high priority targets (Egekwu et al, 2014;Meyer and Hill, 2014).…”

“…(B.) microplus) and their repeat-rich genomes have made complete sequencing, difficult, costly, and time-consuming (Cramaro et al, 2017;Meyer and Hill, 2014;Ullmann et al, 2005). Due to such sustained efforts, omics information is available at web-based resources such as VectorBase (https://www.…”

Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus

“…One explanation for this counter-intuitive result is that the available genomic resources are much greater for I. scapularis than I. ricinus. A complete genome has been published for I. scapularis [48], but only a genome survey is available for I. ricinus [17,49]. For I. ricinus, most proteic sequences in the databases 495 are derived from de novo assembled transcriptomes that are still rather incomplete.…”

Gene Duplication and Protein Evolution in Tick-Host Interactions

“…The only related tick species with extensive genetic data is I. ricinus for which salivary, midgut, and hemocyte transcriptomes were sequenced and a draft genome assembled (Chmelař et al, 2008 ; Schwarz et al, 2013 , 2014b ; Cramaro et al, 2015 , 2017 ; Kotsyfakis et al, 2015a , b ; Perner et al, 2016 ). Molecular clock analysis based on the mitochondrial proteins, suggests that I. scapularis and I. ricinus diverged ~9 MYA, suggesting the majority of the gene duplications detected by Van Zee et al ( 2016 ) occurred after their divergence.…”

“…This could be due to genes missing from the I. scapularis assembly, true duplications in I. ricinus or artifacts from de novo assembled transcriptomes derived from NGS (Mans et al, 2016 ). The genome size of I. ricinus (~2.71 Gbp) is larger than I. scapularis (~2.2 Gbp) (Geraci et al, 2007 ; Cramaro et al, 2017 ), and may explain some of the paralog differences. However, for both species the number and rate of gene duplications are higher than expected, differing by ~5–16-fold from the expected number of gene duplications.…”