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      A dual endosymbiosis supports nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum

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          Abstract

          Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions. Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Fitting Linear Mixed-Effects Models Usinglme4

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              Fast and accurate short read alignment with Burrows–Wheeler transform

              Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                24 December 2021
                2021
                : 10
                : e72747
                Affiliations
                [1 ] MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Univ. Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS) - Institut pour la Recherche et le Développement (IRD) Montpellier France
                [2 ] Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France Montpellier France
                [3 ] Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia Pavia Italy
                [4 ] Faculty of Science, University of South Bohemia České Budějovice Czech Republic
                [5 ] Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot Israel
                [6 ] Department of Biomedical and Clinical Sciences L. Sacco and Pediatric Clinical Research Center, University of Milan Milan Italy
                [7 ] Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Messina Italy
                [8 ] Center of Rickettsiosis and Arthropod-Borne Diseases (CRETAV), San Pedro University Hospital- Center of Biomedical Research from La Rioja (CIBIR) Logroño Spain
                [9 ] Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool Liverpool United Kingdom
                [10 ] Department of Veterinary Medicine, University of Milan Lodi Italy
                École Polytechnique Fédérale de Lausanne Switzerland
                University of Michigan United States
                École Polytechnique Fédérale de Lausanne Switzerland
                École Polytechnique Fédérale de Lausanne Switzerland
                École Polytechnique Fédérale de Lausanne Switzerland
                Yale University United States
                Author notes
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors also contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-8160-2470
                https://orcid.org/0000-0002-1248-9873
                https://orcid.org/0000-0002-5461-5874
                Article
                72747
                10.7554/eLife.72747
                8709577
                34951405
                edd09577-bb70-46bd-89af-2e82ec97349a
                © 2021, Buysse et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 03 August 2021
                : 14 December 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001738, Ministry of Science, Technology and Space;
                Award ID: EVOSYM
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004794, Centre National de la Recherche Scientifique;
                Award ID: EVOSYM
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003977, Israel Science Foundation;
                Award ID: 1074/18
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004412, Human Frontier Science Program;
                Award ID: RGY0075/2017
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003407, Ministry of Education, University and Research;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004794, Centre National de la Recherche Scientifique;
                Award ID: ANR-21-CE02-0002
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Evolutionary Biology
                Custom metadata
                The invasive tick Hyalomma marginatum relies on a dual partner nutritional system to provide B vitamins and avoid nutritional deficiencies due to its exclusive blood diet.

                Life sciences
                endosymbiosis,hematophagy,francisella,midichloria,hyalomma,other
                Life sciences
                endosymbiosis, hematophagy, francisella, midichloria, hyalomma, other

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