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Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

ABSTRACT: High throughput sequencing technologies are revolutionizing genetic research. With this "rise of the machines", genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02-25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.

SUBMITTER: Leese F

PROVIDER: S-EPMC3504011 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

Leese Florian F Brand Philipp P Rozenberg Andrey A Mayer Christoph C Agrawal Shobhit S Dambach Johannes J Dietz Lars L Doemel Jana S JS Goodall-Copstake William P WP Held Christoph C Jackson Jennifer A JA Lampert Kathrin P KP Linse Katrin K Macher Jan N JN Nolzen Jennifer J Raupach Michael J MJ Rivera Nicole T NT Schubart Christoph D CD Striewski Sebastian S Tollrian Ralph R Sands Chester J CJ

PloS one 20121121 11

High throughput sequencing technologies are revolutionizing genetic research. With this "rise of the machines", genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datas ...[more]

PMID: 23185309

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Project description:This is the first comprehensive review of the literature pertaining to Babesia species reported from domestic cats. Description of the four species (Babesia felis, Babesia cati, Babesia herpailuri, and Babesia pantherae) named based on morphology and/or host specificity is documented. Feline babesiosis is of major veterinary concern only in South Africa. Reports of the rare occurrence of feline babesiosis cases in Europe (France, Germany, Poland, and Spain) and Asia (Israel, India, and Pakistan) are documented. Molecular characterization has revealed that cats can harbor a variety of Babesia species. The previous practice of referring to all piroplasms, especially small ones, seen on feline blood smears as B. felis is therefore no longer tenable. The near-full-length 18S rRNA gene sequences entered into GenBank in 2001 (accession no. AF244912) are designated as definitive for B. felis sensu stricto. All published literature relating to molecular characterization of feline Babesia species that could be traced was critically assessed. Four Babesia species are now known to be involved in causing feline babesiosis in South Africa: the closely related B. felis s.s. and Babesia leo (clade I), Babesia lengau (clade II), and Babesia species cat Western Cape (clade VI, Babesia s.s.). Clade VI also includes Babesia canis presentii and Babesia hongkongensis reported from cats in Asia. Six other Babesia species have been reported from domestic cats: the dog-associated B. canis s.s., Babesia gibsoni, and B. vogeli, as well as Babesia lohae, Babesia microti, and Babesia vulpes. Phylogenetic relationships of all named species were assessed and are presented as trees. The relatively high prevalence of B. vogeli in clinically healthy cats (16% in Brazil, 13% on St Kitts, and 8.1% in Portugal) suggests that immunocompetent cats can harbor the infection with no discernible untoward effects. Reports of occurrence of B. felis and other Babesia species in domestic cats should be accepted only if they are supported by credible molecular provenance.

Project description:BackgroundTick-borne pathogens other than Borrelia burgdorferi sensu lato - the causative agent of Lyme borreliosis - are common in Ixodes ricinus ticks. How often these pathogens cause human disease is unknown. In addition, diagnostic tools to identify such diseases are lacking or reserved to research laboratories. To elucidate their prevalence and disease burden, the study 'Ticking on Pandora's Box' has been initiated, a collaborative effort between Amsterdam University Medical Center and the National Institute for Public Health and the Environment.MethodsThe study investigates how often the tick-borne pathogens Anaplasma phagocytophilum, Babesia species, Borrelia miyamotoi, Neoehrlichia mikurensis, spotted fever group Rickettsia species and/or tick-borne encephalitis virus cause an acute febrile illness after tick-bite. We aim to determine the impact and severity of these tick-borne diseases in the Netherlands by measuring their prevalence and describing their clinical picture and course of disease. The study is designed as a prospective case-control study. We aim to include 150 cases - individuals clinically suspected of a tick-borne disease - and 3 matched healthy control groups of 200 persons each. The controls consist respectively of a group of individuals with either a tick-bite without complaints, the general population and of healthy blood donors. During a one-year follow-up we will acquire blood, urine and skin biopsy samples and ticks at baseline, 4 and 12 weeks. Additionally, participants answer modified versions of validated questionnaires to assess self-reported symptoms, among which the SF-36, on a 3 monthly basis.DiscussionThis article describes the background and design of the study protocol of 'Ticking on Pandora's Box'. With our study we hope to provide insight into the prevalence, clinical presentation and disease burden of the tick-borne diseases anaplasmosis, babesiosis, B. miyamotoi disease, neoehrlichiosis, rickettsiosis and tick-borne encephalitis and to assist in test development as well as provide recommendations for national guidelines.Trial registrationNL9258 (retrospectively registered at Netherlands Trial Register, trialregister.nl in in February 2021).

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Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

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Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

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