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      Phylogenomic and biogeographic reconstruction of the Trichinella complex

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          Abstract

          Trichinellosis is a globally important food-borne parasitic disease of humans caused by roundworms of the Trichinella complex. Extensive biological diversity is reflected in substantial ecological and genetic variability within and among Trichinella taxa, and major controversy surrounds the systematics of this complex. Here we report the sequencing and assembly of 16 draft genomes representing all 12 recognized Trichinella species and genotypes, define protein-coding gene sets and assess genetic differences among these taxa. Using thousands of shared single-copy orthologous gene sequences, we fully reconstruct, for the first time, a phylogeny and biogeography for the Trichinella complex, and show that encapsulated and non-encapsulated Trichinella taxa diverged from their most recent common ancestor ∼21 million years ago (mya), with taxon diversifications commencing ∼10−7 mya.

          Abstract

          Trichinellosis is a globally important food-borne disease caused by roundworms of the Trichinella complex. Here the authors present genomic sequences representing all 12 recognized Trichinella species and genotypes, and reconstruct their phylogeny and biogeography.

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          Most cited references 45

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          The impact of next-generation sequencing technology on genetics.

          If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.
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            Genome sequence of the nematode C. elegans: a platform for investigating biology.

             James Mussell (1999)
            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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              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

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                01 February 2016
                2016
                : 7
                Affiliations
                [1 ]Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Melbourne, Victoria 3010, Australia
                [2 ]Istituto Superiore di Sanità , Viale Regina Elena 299, 00161 Rome, Italy
                [3 ]Yourgene Bioscience , Shu-Lin District, New Taipei City 23863, Taiwan
                [4 ]United States National Parasite Collection, US Department of Agriculture, Agricultural Research Service , Beltsville, Maryland 20705, USA
                [5 ]Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800, Australia
                [6 ]Genome Institute of Singapore , 60 Biopolis Street, Singapore 138672, Republic of Singapore
                [7 ]Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School , Singapore 138672, Republic of Singapore
                [8 ]Structural Chemistry Program, Eskitis Institute, Griffith University , Brisbane, Queensland 4111, Australia
                [9 ]Division of Biology, Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, USA
                Author notes
                [*]

                These authors contributed equally to this work.

                Article
                ncomms10513
                10.1038/ncomms10513
                4740406
                26830005
                Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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