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Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing
BACKGROUND: Global 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), t...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299676/ https://www.ncbi.nlm.nih.gov/pubmed/28179027 http://dx.doi.org/10.1186/s13071-017-2008-9 |
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author | Cramaro, Wibke J. Hunewald, Oliver E. Bell-Sakyi, Lesley Muller, Claude P. |
author_facet | Cramaro, Wibke J. Hunewald, Oliver E. Bell-Sakyi, Lesley Muller, Claude P. |
author_sort | Cramaro, Wibke J. |
collection | PubMed |
description | BACKGROUND: Global 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. RESULTS: 235,953 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. CONCLUSIONS: We 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 MATERIAL: The online version of this article (doi:10.1186/s13071-017-2008-9) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5299676 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-52996762017-02-13 Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing Cramaro, Wibke J. Hunewald, Oliver E. Bell-Sakyi, Lesley Muller, Claude P. Parasit Vectors Research BACKGROUND: Global 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. RESULTS: 235,953 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. CONCLUSIONS: We 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 MATERIAL: The online version of this article (doi:10.1186/s13071-017-2008-9) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-08 /pmc/articles/PMC5299676/ /pubmed/28179027 http://dx.doi.org/10.1186/s13071-017-2008-9 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Cramaro, Wibke J. Hunewald, Oliver E. Bell-Sakyi, Lesley Muller, Claude P. Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title | Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title_full | Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title_fullStr | Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title_full_unstemmed | Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title_short | Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing |
title_sort | genome scaffolding and annotation for the pathogen vector ixodes ricinus by ultra-long single molecule sequencing |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299676/ https://www.ncbi.nlm.nih.gov/pubmed/28179027 http://dx.doi.org/10.1186/s13071-017-2008-9 |
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