ActDES – a Curated Actinobacterial Database for Evolutionary Studies

The Actinobacteria are a large diverse phylum of bacteria, often with large genomes with a high G+C content. There is great variation in the sequence quality, equivalence of annotation and phylogenetic representation in the sequence databases meaning that evolutionary and phylogenetic studies may be challenging. To address this, we have assembled a curated, high-level, taxa specific, non-redundant database to aid detailed comparative analysis of Actinobacteria. ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification. <br>Data summary All genome sequences used in this study can be found in the NCBI taxonomy browser https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi and are summarised along with Accession numbers in Table S1<br>1. All other data is available on Figshare.<br>a. Perl script files<br>b. List of genomes from NCBI (Actinobacteria database.xlsx) Table S1<br>c. CVS genome annotation files including the FASTA files of nucleotide and amino acids sequences (612 individual .cvs files – folder cvs)<br>d. BLAST nucleotide database (.fasta file)<br>e. BLAST protein database (.fasta file)<br>f. Table S2 Expansion table genus level (Expansion table.xlsx Tab Genus level)<br>g. Table S2 Expansion table species level (Expansion table.xlsx Tab species level)<br>h. All data for GlcP and Glk data – blast hits from ActDES database, MUSCLE Alignment files and .nwk tree files放线菌门（Actinobacteria）是一类庞大多样的细菌门类，其基因组通常体量较大且G+C含量偏高。当前序列数据库中，序列质量、注释一致性与系统发育代表性存在显著差异，这给进化与系统发育研究带来了不小挑战。为解决这一问题，我们构建了一套经过人工整理、高质量、类群特异性的非冗余数据库，以助力放线菌门的精细比较基因组学（comparative genomics）分析。ActDES是面向放线菌研究者群体的新型资源，主要可应用于两类分析场景：(i) 比较基因组学研究——通过在一组经过筛选、具备系统发育代表性的基因组中实现可靠的直系同源基因（ortholog）鉴定，为该类研究提供有力支撑；(ii) 系统发育基因组学（phylogenomics）研究，通过在指定分类学水平上鉴定基因子集，可有效优化此类分析。上述研究可进一步作为跳板，用于毒力基因进化、代谢进化研究以及代谢工程靶点筛选等方向的探索。 数据汇总：本研究使用的所有基因组序列均可在NCBI分类学浏览器（https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi）获取，相关信息及登录号均汇总于表S1。 1. 其余所有数据均已上传至Figshare平台： a. Perl脚本文件 b. 来自NCBI的基因组列表（Actinobacteria database.xlsx）及表S1 c. 包含核苷酸与氨基酸序列FASTA文件的CVS基因组注释文件（共612个独立.cvs文件，存放于cvs文件夹中） d. BLAST核苷酸数据库（.fasta格式文件） e. BLAST蛋白质数据库（.fasta格式文件） f. 表S2属水平扩展表（Expansion table.xlsx的「Genus level」工作表） g. 表S2种水平扩展表（Expansion table.xlsx的「species level」工作表） h. GlcP与Glk相关的全部数据——包括来自ActDES数据库的BLAST比对结果、MUSCLE比对文件以及.nwk格式的系统发育树文件