• Analysis of the complete genome of the alkaliphilic and phototrophic firmicute Heliorestis convoluta strain HHT

      Dewey, E.D.; Nadendla, S.; Giglio, M.G. (MDPI AG, 2020)
      Despite significant interest and past work to elucidate the phylogeny and photochemistry of species of the Heliobacteriaceae, genomic analyses of heliobacteria to date have been limited to just one published genome, that of the thermophilic species Heliobacterium (Hbt.) modesticaldum str. Ice1T. Here we present an analysis of the complete genome of a second heliobacterium, Heliorestis (Hrs.) convoluta str. HHT, an alkaliphilic, mesophilic, and morphologically distinct heliobacterium isolated from an Egyptian soda lake. The genome of Hrs. convoluta is a single circular chromosome of 3.22 Mb with a GC content of 43.1% and 3263 protein-encoding genes. In addition to culture-based observations and insights gleaned from the Hbt. modesticaldum genome, an analysis of enzyme-encoding genes from key metabolic pathways supports an obligately photoheterotrophic lifestyle for Hrs. convoluta. A complete set of genes encoding enzymes for propionate and butyrate catabolism and the absence of a gene encoding lactate dehydrogenase distinguishes the carbon metabolism of Hrs. convoluta from its close relatives. Comparative analyses of key proteins in Hrs. convoluta, including cytochrome c553 and the Fo alpha subunit of ATP synthase, with those of related species reveal variations in specific amino acid residues that likely contribute to the success of Hrs. convoluta in its highly alkaline environment. Copyright 2020 by the authors.
    • Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae

      Gasser, M.T.; Chung, M.; Bromley, R.E.; Nadendla, S.; Dunning Hotopp, J.C. (American Society for Microbiology, 2019)
      Here, we present the complete genome sequence of the Wolbachia endosymbiont wAna, isolated from Drosophila ananassae and derived from Oxford Nanopore and Illumina sequencing. We anticipate that this will aid in Wolbachia comparative genomics and the assembly of D. ananassae specifically in regions containing extensive lateral gene transfer events. Copyright 2019 Gasser et al.
    • Draft genome sequence of enterobacter sp. Strain olf, a colonizer of olive flies

      Estes, A.M.; Hearn, D.J.; Nadendla, S. (American Society for Microbiology, 2018)
      Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive fruit fly Bactrocera oleae. The 5.07-kbp genome sequence of Enterobacter sp. strain OLF encodes metabolic pathways that allow the bacterium to partially supplement the diet of the olive fly when its dominant endosymbiont, Erwinia dacicola, is absent. Copyright 2018 Estes et al.
    • Draft genome sequence of Erwinia dacicola, a dominant endosymbiont of olive flies

      Estes, A.M.; Hearn, D.J.; Nadendla, S. (American Society for Microbiology, 2018)
      Erwinia dacicola is a dominant endosymbiont of the pestiferous olive fly. Its genome is similar in size and GC content to those of free-living Erwinia species, including the plant pathogen Erwinia amylovora. The E. dacicola genome encodes the metabolic capability to supplement and detoxify the olive fly's diet in larval and adult stages. Copyright 2018 Estes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
    • ECO, the Evidence & Conclusion Ontology: Community standard for evidence information

      Giglio, M.; Tauber, R.; Nadendla, S. (Oxford University Press, 2019)
      The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures and query of evidence. ECO contains over 1500 terms and is in use by many leading biological resources including the Gene Ontology, UniProt and several model organism databases. ECO is continually being expanded and revised based on the needs of the biocuration community. The ontology is freely available for download from GitHub (https://github.com/evidenceontology/) or the projects website (http://evidenceontology. org/). Users can request new terms or changes to existing terms through the projects GitHub site. ECO is released into the public domain under CC0 1.0 Universal. Copyright The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
    • The Gene Ontology resource: Enriching a GOld mine

      Carbon, S.; Chibucos, M.; Giglio, M.; Nadendla, S.; Munro, J.; Jackson, R.; Gene Ontology Consortium (Oxford University Press, 2020-12-08)
      The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations. Copyright The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.