µgreen-db

Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR²/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique <em>genera</em> and 696 unique <em>species</em>). Using µgreen-db, we were able to assign 96 % of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.

研究光合微真核生物与原核蓝细菌群落的生态特征，需借助分子工具以弥补形态学观测的局限性。这类工具依赖特定的遗传标记，且需构建专用数据库以实现分类学归属鉴定。本研究构建了针对23S核糖体RNA（23S rRNA）基因的参考数据库µgreen-db。该数据库的序列来源于通用数据库（NCBI、SILVA）与比较RNA数据库（Comparative RNA Web, CRW），同时采用了更具创新性的递归BLAST（局部序列比对搜索工具）搜索策略，以实现最优的序列回收效果。截至目前，基于NCBI与AlgaeBase的分类系统，µgreen-db共收录2326条23S rRNA序列，涵盖真核生物与原核生物类群，包含光合微真核生物、蓝细菌以及非维管陆生植物共计442个独立属与736个物种；若采用PR²/SILVA分类系统，则µgreen-db共收录2217条序列，涵盖399个独立属与696个物种。利用µgreen-db，我们可将土壤DNA扩增后通过宏条形码（metabarcoding）测序获得的23S rRNA基因V区序列中96%的序列在属水平完成分类鉴定，充分体现了该数据库良好的覆盖度。µgreen-db的访问地址为http://microgreen-23sdatabase.ea.inra.fr。