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• 1. [Article] A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick

  Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern ...

  Citation × Citation Citation Abstract Copy Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Close

• 2. [Article] Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content

  Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish ...

  Citation × Citation Citation Abstract Copy Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Close