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      Complete genome sequence of Liberibacter crescens BT-1

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          Abstract

          Liberibacter crescens BT-1, a Gram-negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya to gain insight on Huanglongbing (HLB) and Zebra Chip (ZC) diseases. The genome of BT-1 was sequenced at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. A finished assembly and annotation yielded one chromosome with a length of 1,504,659 bp and a G+C content of 35.4%. Comparison to other species in the Liberibacter genus, L. crescens has many more genes in thiamine and essential amino acid biosynthesis. This likely explains why L. crescens BT-1 is culturable while the known Liberibacter strains have not yet been cultured. Similar to Candidatus L. asiaticus psy62, the L. crescens BT-1 genome contains two prophage regions.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            The minimum information about a genome sequence (MIGS) specification.

            Dawn Field, George Garrity, Tanya Gray … (2008)
            With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
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              The Pfam protein families database.

              A. Bateman, E. Birney, R. Durbin … (2000)
              Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/. The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (iso-abbrev): Stand Genomic Sci
                Journal ID (publisher-id): SIGS
                Title: Standards in Genomic Sciences
                Publisher: Michigan State University
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 12 December 2012
                Publication date Collection: 19 December 2012
                Volume: 7
                Issue: 2
                Pages: 271-283
                Affiliations
                [1 ]Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
                [2 ]Plant Pathology Department, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, Lake Alfred, FL, USA
                Article
                Publisher ID: sigs.3326772
                DOI: 10.4056/sigs.3326772
                PMC ID: 3569387
                PubMed ID: 23408754
                SO-VID: 8ef9c725-ca03-412e-bc49-da94ee1ed91b
                Copyright © Copyright © retained by original authors.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Keywords: huanglongbing,citrus greening,reduced genome,fastidious,hybrid assembly
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: huanglongbing, citrus greening, reduced genome, fastidious, hybrid assembly

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