The highly improved genome ofIxodes scapulariswith X and Y pseudochromosomes

Abstract

Ixodes scapularis, the black-legged tick, is the principal vector of the Lyme disease spirochete,Borrelia burgdorferi, and is responsible for most of the ∼470,000 estimated Lyme disease cases annually in the USA.Ixodes scapulariscan transmit six additional pathogens of human health significance. Because of its medical importance,I. scapulariswas the first tick genome to be sequenced and annotated. However, the first assembly,I. scapularisWikel (IscaW), was highly fragmented because of the technical challenges posed by the long, repetitive genome sequences characteristic of arthropod genomes and the lack of long-read sequencing techniques. AlthoughI. scapularishas emerged as a model for tick research because of the availability of new tools such as embryo injection and CRISPR-Cas9-mediated gene editing yet the lack of chromosome-scale scaffolds has slowed progress in tick biology and the development of tools for their control. Here we combine diverse technologies to produce theI. scapularisGulia-Nuss (IscGN) genome assembly and gene set. We used DNA from eggs and male and female adult ticks and took advantage of Hi-C, PacBio HiFi sequencing, and Illumina short-read sequencing technologies to produce a chromosome-level assembly. In this work, we present the predicted pseudochromosomes consisting of 13 autosomes and the sex pseudochromosomes: X and Y, and a markedly improved genome annotation compared with the existing assemblies and annotations.

Validation of a heat-inducibleIxodes scapularisHSP70 promoter and developing a tick-specific 3xP3 promoter sequence in ISE6 cells

“…Using blastp, we identified a putative ortholog of HSP70: ISCW024910 in the I. scapularis Wikel genome with greater than 70% amino acid sequence identity and consisted of a single exon. We confirmed this sequence with our highly contiguous genome assembly ( Nuss et al, 2023 ). We located an intergenic sequence 5’ from the coding region of these genes and confirmed potential promoter function by bioinformatics analysis (data not shown) ( Shahmuradov and Solovyev, 2015; Solovyev and Shahmuradov, 2003 ) (Figures 1, 2).…”

The repetitive genome of theIxodes ricinustick reveals transposable elements have driven genome evolution in ticks

“…We have generated two high-quality genome assemblies for the major disease vector I. ricinus. These assemblies have comparable quality to the genomes of other tick species such as I. scapularis 20,21 and I. persulcatus 24 . The genome size of I. ricinus is approximately 2.15 Gbp.…”

“…While I. ricinus is of medical and veterinary importance, we have only a preliminary understanding of its genome. The current I. ricinus genome assembly 19 is partial (Table 1), covering only a quarter of the expected size relative to the genome assemblies for the other major Lyme borreliosis tick vector and sister species, I. scapularis 20,21 . This lack of tick genome assemblies impedes comparative analyses of major tick vectors.…”

“…This lack of tick genome assemblies impedes comparative analyses of major tick vectors. The genomes of ticks have been challenging to assemble due in part to their large genome sizes, abundant biological genome contamination and genome complexity [20][21][22][23][24][25][26] . In particular, a large proportion of tick genomes are repetitive, with repeats comprising more than two-thirds of the genome in Ixodes species 20,24,27 .…”

“…The vertical dashed line indicates the approximate divergence time between I. ricinus and I. scapularis of 13 million years ago31 .DISCUSSIONWe have generated two high-quality genome assemblies for the major disease vector I. ricinus. These assemblies have comparable quality to the genomes of other tick species such as I. scapularis20,21 and I. persulcatus24 . The genome size of I. ricinus is approximately 2.15 Gbp.…”