Innuendo Whole Genome And Core Genome Mlst Schemas And Datasets For Yersinia Enterocolitica

<strong>Dataset</strong> All the raw reads deposited in the European Nucleotide Archive (ENA) or in the NCBI Sequence Read Archive (SRA) as <em>Y. enterocolitica</em> at the time of the analysis (August 2018) were retrieved using getSeqENA. A total of 252 genomes were successfully assembled using INNUca v3.1. In addition to public available genomes, the database includes 79 novel <em>Y. enterocolitica</em> strains which belong to the INNUENDO Sequence Dataset (PRJEB27020). File 'Metadata/Yenterocolitica_metadata.txt' contains metadata information for each strain including country and year of isolation, source classification, taxon of the host, serotype, biotype, pathotype (according to patho_typing software) and classical pubMLST 7 genes ST according to Hall et al., 2005. The directory 'Genomes' contains all the 331 INNUca V3.1 assemblies of the strains listed in 'Metadata/Yenterocolitica_metadata.txt'. <strong>Schema creation and validation</strong> All the 331 genomes were used for creating the schema using <strong>chewBBACA suite</strong>. The quality of the loci have been assessed using <em>chewBBACA Schema Evaluation</em> and loci with single alleles, those with high length variability (i.e. if more than 1 allele is outside the mode +/- 0.05 size) and those present in less than 1% of the genomes have been removed. The wgMLST schema have been further curated, excluding all those loci detected as “Repeated Loci” and loci annotated as “non-informative paralogous hit (NIPH/ NIPHEM)” or “Allele Larger/ Smaller than length mode (ALM/ ASM)” by the <em>chewBBACA Allele Calling</em> in more than 1% of a dataset. File 'Schema/Yenterocolitica_wgMLST_ 6344_schema.tar.gz' contains the wgMLST schema formatted for chewBBACA and includes a total of 6,344 loci. File 'Schema/Yenterocolitica_cgMLST_ 2406_listGenes.txt' contains the list of genes from the wgMLST schema which defines the cgMLST schema. The cgMLST schema consists of 2,406 loci and has been defined as the loci present in at least the 99% of the 331<em> Y. enterocolitica</em> genomes. Genomes have no more than 2% of missing loci. File 'Allele_Profles/Yenterocolitica_wgMLST_alleleProfiles.tsv' contains the wgMLST allelic profile of the 331 <em>Y. enterocolitica</em> genomes of the dataset. Please note that missing loci follow the annotation of chewBBACA Allele Calling software. File 'Allele_Profles/Yenterocolitica_cgMLST_alleleProfiles.tsv' contains the cgMLST allelic profile of the 331 <em>Y. enterocolitica</em> genomes of the dataset. Please note that missing loci are indicated with a zero. <strong>Additional citation</strong> The schema are prepared to be used with <strong>chewBBACA</strong>. When using the schema in this repository please cite also: Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. 15/03/2018. M Gen 4(3): doi:10.1099/mgen.0.000166 http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166**数据集** 本研究检索了截至分析时（2018年8月）提交至欧洲核苷酸档案库（European Nucleotide Archive, ENA）或NCBI序列读取档案库（NCBI Sequence Read Archive, SRA）的所有标注为小肠结肠炎耶尔森菌（*Y. enterocolitica*）的原始测序读段，检索过程通过getSeqENA工具完成。最终使用INNUca v3.1工具成功组装得到252个基因组序列。除公开可用的基因组外，本数据库还包含79株全新的小肠结肠炎耶尔森菌（*Y. enterocolitica*）菌株，均隶属于INNUENDO序列数据集（登录号：PRJEB27020）。 元数据文件`Metadata/Yenterocolitica_metadata.txt`包含各菌株的详细元数据信息，具体包括分离国家与年份、来源分类、宿主类群、血清型、生物型、致病型（基于patho_typing软件鉴定）以及依据Hall等人2005年研究设定的经典pubMLST 7个基因的序列型（ST）。 `Genomes`目录包含了元数据文件中列出的全部331株菌株经INNUca V3.1组装得到的基因组序列。 **数据库架构构建与验证** 本研究使用**chewBBACA工具套件**，基于全部331个基因组序列构建分型架构。通过<em>chewBBACA架构评估模块</em>对位点质量进行评估，最终剔除仅含单等位基因、长度变异程度过高（即超过1个等位基因偏离众数大小±0.05范围）以及在少于1%的基因组中存在的位点。进一步对全基因组多位点序列分型（wgMLST）架构进行人工校正，剔除在超过1%的数据集样本中被<em>chewBBACA等位基因分型模块</em>判定为“重复位点”，或被注释为“非信息性旁系同源比对（NIPH/NIPHEM）”、“等位基因长度偏离众数过大/过小（ALM/ASM）”的位点。 `Schema/Yenterocolitica_wgMLST_6344_schema.tar.gz`文件为适配chewBBACA工具格式的wgMLST分型架构，共包含6344个位点。 `Schema/Yenterocolitica_cgMLST_2406_listGenes.txt`文件包含了构成核心基因组多位点序列分型（cgMLST）架构的wgMLST位点列表。该cgMLST架构共包含2406个位点，定义为在至少99%的331株小肠结肠炎耶尔森菌（*Y. enterocolitica*）基因组中均存在的位点，且单株基因组中缺失的位点比例不超过2%。 `Allele_Profles/Yenterocolitica_wgMLST_alleleProfiles.tsv`文件包含本数据集331株小肠结肠炎耶尔森菌的wgMLST等位基因分型谱。请注意：缺失位点的标注规则遵循chewBBACA等位基因分型软件的输出格式。 `Allele_Profles/Yenterocolitica_cgMLST_alleleProfiles.tsv`文件包含本数据集331株小肠结肠炎耶尔森菌的cgMLST等位基因分型谱。请注意：缺失位点以数字0标注。 **附加引用说明** 本分型架构专为配合**chewBBACA**工具使用而构建。若使用本仓库中的分型架构，请同时引用以下文献： Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA：一款用于逐基因分型架构构建与菌株鉴定的完整工具套件. 2018年3月15日. M Gen 4(3): doi:10.1099/mgen.0.000166 详见：http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166