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      The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

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          Abstract

          Background

          The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.

          Results

          The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.

          Conclusions

          The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.

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          Most cited references85

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          Genome sequence of the nematode C. elegans: a platform for investigating biology.

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          The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes.
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            TCDB: the Transporter Classification Database for membrane transport protein analyses and information

            The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10 000 references, encompassing ∼3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at . The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.
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              Draft genome of the filarial nematode parasite Brugia malayi.

              Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.
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                Author and article information

                Contributors
                Journal
                Genome Biol
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2013
                28 August 2013
                : 14
                : 8
                : R89
                Affiliations
                [1 ]Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
                [2 ]Faculty of Veterinary Science, The University of Melbourne, Corner of Flemington Road and Park Drive, Parkville, Victoria 3010, Australia
                [3 ]Current address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853-2703, USA
                [4 ]Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824, USA
                [5 ]Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, 48824, USA
                [6 ]Eskitis Institute for Cell and Molecular Therapies, Griffith University, N75 Don Young Road, Brisbane Innovation Park, Nathan, Queensland 4111, Australia
                [7 ]Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
                [8 ]State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 1 Xujiaping, Yanchangbu, Lanzhou, Gansu Province 730046, PR China
                [9 ]Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
                [10 ]Center for Biodiscovery and Molecular Development of Therapeutics, Queensland Tropical Health Alliance, James Cook University, Cairns, Queensland 4870, Australia
                Article
                gb-2013-14-8-r89
                10.1186/gb-2013-14-8-r89
                4053716
                23985341
                6577a6a2-d2b7-4927-840e-ebca1cd0fbba
                Copyright © 2013 Schwarz et al.; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://http//creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research

                Genetics
                Genetics

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