Author
Stephen C. Barker
Other affiliations: Macquarie University, Queensland Museum, Centre for Cellular and Molecular Biology ...read more
Bio: Stephen C. Barker is an academic researcher from University of Queensland. The author has contributed to research in topics: Genome & Louse. The author has an hindex of 57, co-authored 178 publications receiving 8693 citations. Previous affiliations of Stephen C. Barker include Macquarie University & Queensland Museum.
Topics: Genome, Louse, Tick, Ixodidae, Phylogenetic tree
Papers published on a yearly basis
Papers
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J. Craig Venter Institute1, Broad Institute2, University of Illinois at Urbana–Champaign3, Bangor University4, University of Reading5, University of Massachusetts Amherst6, Seoul National University7, University of Notre Dame8, University of Houston9, Swiss Institute of Bioinformatics10, University of Geneva11, Georgetown University12, Texas A&M University13, Purdue University14, University of Bordeaux15, University of Santiago de Compostela16, National Institutes of Health17, University of Barcelona18, Wayne State University19, University of Florida20, Miami University21, Kansas State University22, Ohio State University23, Centers for Disease Control and Prevention24, Rio de Janeiro State University25, University of Queensland26, Imperial College London27
TL;DR: The genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola are presented, providing a reference for studies of holometabolous insects.
Abstract: As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
498 citations
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TL;DR: This work is intended as a consensus list of valid tick names, following recent revisionary studies, wherein it recognizes 896 species of ticks in 3 families.
Abstract: This work is intended as a consensus list of valid tick names, following recent revisionary studies, wherein we recognize 896 species of ticks in 3 families. The Nuttalliellidae is monotypic, containing the single entity Nuttalliella namaqua. The Argasidae consists of 193 species, but there is widespread disagreement concerning the genera in this family, and fully 133 argasids will have to be further studied before any consensus can be reached on the issue of genus-level classification. The Ixodidae comprises 702 species in 14 genera: Amblyomma (130 species, of which 17 were formerly included in Aponomma, a genus that is still considered valid by some authors), Anomalohimalaya (3), Bothriocroton (7, all previously included in Aponomma), Cosmiomma (1), Cornupalpatum (1), Compluriscutula (1), Dermacentor (34, including the single member of the former genus Anocentor, which is still considered valid by some authors), Haemaphysalis (166), Hyalomma (27), Ixodes (243), Margaropus (3), Nosomma (2), Rhipicentor (2) and Rhipicephalus (82, including 5 species from the former genus Boophilus, which is still considered valid by some authors). We regard six names as invalid: Amblyomma laticaudae Warburton, 1933 is a synonym of Amblyomma nitidum Hirst & Hirst, 1910; Bothriocroton decorosum (Koch, 1867) is a synonym of B. undatum (Fabricius, 1775); Haemaphysalis vietnamensis Hoogstraal & Wilson, 1966 is a synonym of H. colasbelcouri (Santos Dias, 1958); Haemaphysalis xinjiangensis Teng, 1980 is a synonym of H. danieli C erný & Hoogstraal, 1977; Hyalomma erythraeum Tonelli-Rondelli, 1932 is a synonym of H. impeltatum Schulze and Schlottke, 1930 and Rhipicephalus hoogstraali Kolonin, 2009 was not described according to the rules of the International Code of Zoological Nomenclature.
487 citations
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University of Nevada, Reno1, Purdue University2, Monsanto3, Old Dominion University4, North Carolina State University5, University College London6, Oklahoma State University–Stillwater7, Spanish National Research Council8, National Institutes of Health9, Wellcome Trust10, University of Cambridge11, J. Craig Venter Institute12, Leidos13, Broad Institute14, University of Nevada, Las Vegas15, University of Notre Dame16, University of Barcelona17, Carlos III Health Institute18, University of Massachusetts Medical School19, University of Connecticut20, University of Oxford21, University of Lausanne22, Virginia Tech23, West Virginia University24, Indiana University25, University of Maryland, Baltimore26, Texas A&M University27, Kansas State University28, University of Minnesota29, University of Manchester30, National University of Singapore31, University of California, San Francisco32, Iowa State University33, Colorado State University34, Pennsylvania State University35, University of California, Riverside36, Max Planck Society37, ANSES38, University of Santiago de Compostela39, Pompeu Fabra University40, California State Polytechnic University, Pomona41, University of Queensland42, University of the Sunshine Coast43, Swiss Institute of Bioinformatics44, University of Geneva45, University of Copenhagen46, University of Tennessee Health Science Center47, University of Vigo48, Wellcome Trust Sanger Institute49, University of Illinois at Urbana–Champaign50, Quinnipiac University51, International Livestock Research Institute52
TL;DR: Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported.
Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
406 citations
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TL;DR: For a list of the 899 valid genus and species names of ticks as of February 2004, see, e.g., the authors, for example, the list presented in this paper.
Abstract: In recent years there has been much progress in our understanding of the phylogeny and evolution of ticks, in particular the hard ticks (Ixodidae). Indeed, a consensus about the phylogeny of the hard ticks has emerged which is quite different to the working hypothesis of 10 years ago. So that the classification reflects our knowledge of ticks, several changes to the nomenclature of ticks are imminent or have been made. One subfamily, the Hyalomminae, should be sunk, while another, the Bothriocrotoninae, has been created (Klompen, Dobson & Barker, 2002). Bothriocrotoninae, and its sole genus Bothriocroton, have been created to house an early-diverging ('basal') lineage of endemic Australian ticks that used to be in the genus Aponomma. The remaining species of the genus Aponomma have been moved to the genus Amblyomma. Thus, the name Aponomma is no longer a valid genus name. The genus Rhipicephalus is paraphyletic with respect to the genus Boophilus. Thus, the genus Boophilus has become a subgenus of the genus Rhipicephalus (Murrell & Barker, 2003). Knowledge of the phylogenetic relationships of ticks has also provided new insights into the evolution of ornateness and of their life cycles, and has allowed the historical zoogeography of ticks to be studied. Finally, we present a list of the 899 valid genus and species names of ticks as of February 2004.
325 citations
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TL;DR: The addition of ribosomal and transfer RNA genes to the protein coding genes traditionally used in mitochondrial genome phylogenies improved the resolution and support, contrary to previous suggestions that these genes would evolve too quickly or prove too difficult to align to provide phylogenetic signal at deep nodes.
Abstract: Mitochondrial genomes provide a promising new tool for understanding deep-level insect phylogenetics, but have yet to be evaluated for their ability to resolve intraordinal relationships. We tested the utility of mitochondrial genome data for the resolution of relationships within Diptera, the insect order for which the most data are available. We sequenced an additional three genomes, from a syrphid, nemestrinid and tabanid, representing three additional dipteran clades, 'aschiza', non-heteroneuran muscomorpha and 'basal brachyceran', respectively. We assessed the influence of optimality criteria, gene inclusion/exclusion, data recoding and partitioning strategies on topology and nodal support within Diptera. Our consensus phylogeny of Diptera was largely consistent with previous phylogenetic hypotheses of the order, except that we did not recover a monophyletic Muscomorpha (Nesmestrinidae grouped with Tabanidae) or Acalyptratae (Drosophilidae grouped with Calliphoridae). The results were very robust to optimality criteria, as parsimony, likelihood and Bayesian approaches yielded very similar topologies, although nodal support varied. The addition of ribosomal and transfer RNA genes to the protein coding genes traditionally used in mitochondrial genome phylogenies improved the resolution and support, contrary to previous suggestions that these genes would evolve too quickly or prove too difficult to align to provide phylogenetic signal at deep nodes. Strategies to recode data, aimed at reducing homoplasy, resulted in a decrease in tree resolution and branch support. Bayesian analyses were highly sensitive to partitioning strategy: biologically realistic partitions into codon groups produced the best results. The implications of this study for dipteran systematics and the effective approaches to using mitochondrial genome data are discussed. Mitochondrial genomes resolve intraordinal relationships within Diptera accurately over very wide time ranges (1-200 million years ago) and genetic distances, suggesting that this may be an excellent data source for deep-level studies within other, less studied, insect orders.
252 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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TL;DR: The comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages.
Abstract: Animal mitochondrial DNA is a small, extrachromosomal genome, typically ~16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems—‘mitochondrial genomics’— serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.
2,923 citations
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Commonwealth Scientific and Industrial Research Organisation1, Rutgers University2, Heidelberg Institute for Theoretical Studies3, University of Jena4, University of Bonn5, University of Vienna6, Naturhistorisches Museum7, University of Tsukuba8, Landcare Research9, Johns Hopkins University10, University of Hamburg11, Ehime University12, Florida Museum of Natural History13, Staatliches Museum für Naturkunde Stuttgart14, National Evolutionary Synthesis Center15, Macquarie University16, Australian National University17, American Museum of Natural History18, University of Memphis19, University of Guadalajara20, Bavarian Academy of Sciences and Humanities21, Natural History Museum22, Karlsruhe Institute of Technology23, California Academy of Sciences24, South China Agricultural University25, North Carolina State University26, Hokkaido University27
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
1,998 citations