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      Draft genome sequence of Colletotrichum sansevieriae Sa-1–2, the anthracnose pathogen of Sansevieria trifasciata

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      Author(s): a , * , b , a , a
      Publication date (Electronic):
      Journal: Data in Brief
      Publisher: Elsevier

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          Abstract

          Colletotrichum sansevieriae is an ascomycete fungus causing anthracnose disease on plants in the genus Sansevieria. Here, we report the draft genome sequence of isolate Sa-1–2 of this fungus. The genome size is >51 Mb, and the assembly consists of 8647 contigs and contains 13,664 predicted protein-coding genes. Pathogenicity factors such as plant cell wall-degrading enzymes and effector proteins were also predicted. Additionally, the phylogenetic relationship of isolates from different Colletotrichum spp. was analyzed, revealing that the isolate belongs to a novel major clade consisting of species that infect succulent plants originating from Africa. The draft genome sequence has been deposited at GenBank under accession number NJHP00000000.

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          A new generation of homology search tools based on probabilistic inference.

          Sean R. Eddy (2009)
          Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST's programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST's speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.
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            WWW-query: an on-line retrieval system for biological sequence banks.

            M Gouy, G Perrière (1995)
            We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.
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              Anthracnose of Sansevieriatrifasciata caused by Colletotrichumsansevieriae sp. nov.

              M. NAKAMURA, M. Ohzono, H Iwai … (2006)
              Article 0 comments Cited 9 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Masayuki Nakamura
                Journal
                Journal ID (nlm-ta): Data Brief
                Journal ID (iso-abbrev): Data Brief
                Title: Data in Brief
                Publisher: Elsevier
                ISSN (Electronic): 2352-3409
                Publication date PMC-release: 21 March 2018
                Publication date Collection: June 2018
                Publication date (Electronic): 21 March 2018
                Volume: 18
                Pages: 691-695
                Affiliations
                [a ]Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
                [b ]Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-8605, Japan
                Author notes
                [* ]Corresponding author. masa@ 123456agri.kagoshima-u.ac.jp
                Article
                Publisher ID: S2352-3409(18)30296-8
                DOI: 10.1016/j.dib.2018.03.083
                PMC ID: 5996722
                SO-VID: 0707bcfe-af1d-4645-be31-33d98c807332
                Copyright © © 2018 The Authors
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 16 January 2018
                Date revision received : 17 February 2018
                Date accepted : 16 March 2018
                Categories
                Subject: Genetics, Genomics and Molecular Biology

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