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      Complete mitogenome of the dog cucumber tapeworm Dipylidium caninum (Cestoda, Dilepididae) from Southwest China

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          Abstract

          The cucumber tapeworm Dipylidium caninum (Cestoda, Dilepididae) is a common intestinal parasite of dogs and cats and can cause dipylidiasis in humans, especially in infants and children. In this study, the complete mitogenome of this tapeworm was sequenced using next-generation sequencing technology. The entire genome was 14,226 bp in size and encoded 36 genes, including 12 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The phylogeny revealed that D. caninum grouped with other species from the order Cyclophyllidea and separated from species of Pseudophyllidea. Within the Dipylidiidae, both dog-originated D. caninum were phylogenetic distinctiveness from cat-originated D. caninum, suggesting that D. caninum may represent a species complex. Altogether, the complete mitogenome of D. caninum sequenced here should contribute to a better understanding of the phylogenetic and taxonomic placement of this species.

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          Most cited references 11

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          MITOS: improved de novo metazoan mitochondrial genome annotation.

          About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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            Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

            We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
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              Replication and transcription of vertebrate mitochondrial DNA.

               D Clayton (1990)
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                22 July 2019
                2019
                : 4
                : 2
                : 2670-2672
                Affiliations
                [a ]Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China;
                [b ]Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, China;
                [c ]Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
                Author notes
                [*]

                These authors contributed equally to this work.

                CONTACT Yue Xie xyue1985@ 123456gmail.com Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu611130, China
                Article
                1644236
                10.1080/23802359.2019.1644236
                7706460
                © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1358
                Product
                Categories
                Research Article
                Mitogenome Announcement

                dipylidium caninum, mitogenome, phylogeny

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