Table of Contents: :: Library Catalog

Saved in:

Bibliographic Details
Main Authors:	Kostarnoy, Alexey, Grumov, Daniil, Gancheva, Petya
Format:	Recurso digital
Language:
Published:	Zenodo 2026
Online Access:	https://doi.org/10.5281/zenodo.19921276
Tags:	Add Tag No Tags, Be the first to tag this record!

Table of Contents:

Here we provide the genome assembly and genome annotation of Dermacentor reticulatus tick.  High-molecular-weight DNA was extracted from an unfed female D. reticulatus collected in the Caucasus Mountains (Russia, Republic of Dagestan, collection date 15-17.09.2024, latitude 41.376603 N, longitude 47.721245 E, elevation (meters above sea level) – 1573 meters, biome temperate broadleaf & mixed forests, ecoregion - Caucasus mixed forests, description of biotope (made at time of tick collection) - grassland and shrubland on the mountain slope). The whole tick was ground using a mortar and pestle under liquid nitrogen. The resulting homogenate was transferred into microcentrifuge tubes containing CTAB extraction buffer (100 mM Tris pH 8.0, 20 mM EDTA, 1.4 M NaCl). After 10 minutes, β-mercaptoethanol (was added to the homogenate to a final concentration of 1%, followed by incubation at room temperature for 10–15 minutes. The tubes were then placed on a rotary thermoshaker and incubated for 20 minutes at 56 °C. Proteinase K was added at a volume of 10 μL per 500 μL of CTAB buffer, and the mixture was incubated for 3 hours at 56 °C. Following incubation, an equal volume of chloroform was added to the lysate. The mixture was vortexed for 10 seconds and centrifuged at 14,000 × g for 10 minutes to ensure complete phase separation. The aqueous phase was carefully transferred to a new tube, and the extraction step was repeated. The final aqueous phase was transferred to a new tube, and the nucleic acids were precipitated by adding 0.7 volumes of isopropanol, followed by incubation at −20 °C for 1 hour. The sample was centrifuged at 14,000 × g for 15 minutes, after which the supernatant was discarded. The nucleic acid pellet was subsequently washed twice with 500 μL of cold 80% ethanol. The pellet was then air-dried at room temperature to remove residual ethanol and resuspended in 200 μL of TE buffer. The DNA was quantified using a Qubit 4 Fluorometer and a Nanodrop ND-1000, and its quality was assessed by electrophoresis on a 1% agarose gel and using an Agilent 2100 Bioanalyzer according to the manufacturer's instructions. The extracted DNA was divided into two aliquots. One aliquot was used for Nanopore sequencing, and another aliquot was used for PacBio sequencing. The genome was assembled using ONT and PacBio reads with Hifiasm v0.25.0-r726. Assembly quality was assessed using BUSCO v5.8.3 with the reference dataset ‘arachnida_odb12’. PacBio and ONT reads were mapped to the assembly using minimap2 v2.26-r1175. For taxonomic validation, the scaffolds were queried against the NCBI NT database (Release 2025-05-18) using BLASTn v2.16.0+ and against the UniProt database (Release 2025_03, 18-Jun-2025) using DIAMOND BLASTx v2.1.12. Further statistics gathering and consolidation and visualization were performed with BlobToolKit v4.4.5. Scaffolds were assigned to pseudochromosomes using RagTag v2.1.0 with the chromosome-level D. silvarum BIME_Dsil_1.4 reference assembly (GCA_013339745.2). Early was published that various Dermacentor spp. including D. silvarum possess ten autosomal chromosomes and one sex chromosome, and we construct 11 pseudochromosomes. Protein-coding genes were predicted using the NCBI Eukaryotic Genome Annotation Pipeline–External. Nucleotide-level synteny between the assembly and the reference was assessed by aligning the scaffolds to the D. silvarum chromosomes with minimap2 v2.30 and visualized in R using circlize v0.4.17.

Similar Items