- Pseudocohnilembus persalinus genome database - the first genome database of facultative scuticociliatosis pathogens. - Background: Pseudocohnilembus persalinus , a unicellular ciliated protozoan, is one of commonest facultative pathogens. - persalinus genome database (PPGD) (http://ciliates.ihb.ac.cn/database/home/#pp), the first genome database for the scuticociliatosis pathogens. - We will continue to update the PPGD by integrating more data and aim to integrate the PPGD with other ciliate databases to build a comprehensive ciliate genome database.. - Keywords: Pseudocohnilembus persalinus , Genome database, Useful resource, Scuticociliate. - The Pseudocohnilembus persalinus scuticociliate is a free-living marine ciliate first reported by Evans and Thompson in 1964 [1]. - persalinus infection causes scuti- cociliatosis, one of the most important fish diseases that has led to serious economic losses in marine aquaculture worldwide [5, 6]. - persalinus is a facul- tative parasite and can be easily grown in the labora- tory by feeding with bacteria. - Before that, the genomes of Tetrahymena thermophila , Paramecium tetraurelia and Ichthyo phthirius multifiliis have first been sequenced and their comparative genomics analyses have compre- hensively provided a better understanding of the. - 1 Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Full list of author information is available at the end of the article. - 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - persalinus genome database (PPGD), which integrates genomic data, transcriptomic data, and gene annotation, thereby providing a useful resource for studying scuticocili- ates or scuticociliatosis.. - Figure 1 shows a schematic diagram of the structure of the PPGD. - Genomic sequence data, transcriptomic se- quence (RNA-Seq) data, and genome annotation data are stored in the MySQL database. - The user-friendly interface and web pages were developed with PHP and HTML. - The PPGD also includes a brief summary of the biological, morphological, and taxonom- ical characteristics of P. - 1 Diagram of the PPGD. - Sequence data, gene annotation, and RNA-Seq data were stored in the MySQL database, and also presented by GBrowse. - Meanwhile, search functions enable the user to easily access the resources in PPGD. - For all the 13,186 predicted genes of genes have more or less reads mapped in the growth condition. - “SEARCH,” “GENOME BROWSER,” “BLAST,” “MORP HOLOGY,” and “DATA DOWNLOAD”) directs the user to retrieve the information. - The “HOME” page displays some background information on P. - A search box (located at the top right of the web page. - 2a) enables the user to search for “Gene ID,” “Keywords,” or “Scaffold ID” in the database (Fig. - We recommend searching the database using a “Gene ID”. - The search hits are listed and hy- perlinks direct the user to detailed information about the gene. - 2 Basic search functions of the PPGD. - a A basic search function using the “ Gene ID. - Typically, the user can use “Gene ID” or a scaffold. - GBrowse provides the user with informa- tion on the gene structure and expression levels. - In the gene model track, a hyperlink forwards the user to a web page with more detailed gene information.. - In addition, once an interesting gene or genomic region is selected, the user can scroll and zoom using the navigation bar (shown in the upper right of Fig. - The sequence can also be retrieved in FASTA format by selecting the “Download Deco- rated FASTA File ” option in the drop-down menu in GBrowse.. - The “MORPHOLOGY” page of PPGD displays detailed morphological information and the taxonomic status of P. - to integrate these into PPGD to build a comprehen- sive genome database for ciliates.. - PPGD is the first genome database for a scuticociliate. - PPGD: Pseudocohnilembus persalinus genome database. - 31672281) to JX, Knowledge Innovation Program of the Chinese Academy of Sciences to JX, Youth Innovation Promotion Association of the Chinese Academy of Sciences to JX.. - The database is freely available at http://ciliates.ihb.ac.cn/database/home/#pp.. - All authors have approved the final version of the manuscript.. - Morphogenesis in the hymenostome ciliate Pseudocohnilembus persalinus and its taxonomic and phylogenetic implications. - Pseudocohnilembus persalinus (Ciliophora : Scuticociitida) is an additional species causing scuticociliatosis in olive flounder Paralichthys olivaceus . - Studies on the morphology of Uronema marinum Dujardin (Ciliatea: Uronematidae) with a description of the histopathology of the infection in marine fishes. - Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer. - accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. - Stomatogenesis and morphological redescription of Pseudocohnilembus persalinus (Ciliophora:. - Identification of the pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization. - The all- data-based evolutionary hypothesis of ciliated protists with a revised classification of the phylum Ciliophora (eukaryota, Alveolata)
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