PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy
PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy
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DOI：
10.1111/1755-0998.12401
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发表时间：
2015-11-01
影响因子：
7.7
通讯作者：
Christen, Richard
中科院分区：
文献类型：
--
作者：
Decelle, Johan;Romac, Sarah;Christen, Richard
光合真核生物在生物圈的大多数生态系统中作为主要生产者发挥着关键作用。正在进行的环境元条形码革命打开了这些生物的整体生态系统生物学研究的前景，特别是单细胞微藻，往往缺乏独特的形态特征，并具有复杂的生命周期。为了解释环境序列，元条形码编码必须依赖于分类学上策划的数据库，该数据库包含来自已鉴定生物体的靶基因（或条形码）的参考序列。到目前为止，没有这样的参考框架存在的光合真核生物。在这项研究中，我们建立了PhytoREF数据库，其中包含6490个质体16S rDNA参考序列，这些序列来自代表所有已知主要光合谱系的大量真核生物。我们编译了3333个扩增子序列，可从公共数据库和879个序列提取的质体基因组，并产生了411个新的序列，从培养的海洋微藻株属于不同的真核细胞谱系。数据库中还包括1867个环境桑格16 S rDNA序列。对每个16S rDNA序列应用严格的质量过滤和基于遗传学的分类学分类。该数据库主要侧重于海洋微藻，但也包括陆地植物序列（占PhytoREF序列的一半）和淡水分类群，以扩大PhytoREF对不同水生和陆地生境的适用性。PhytoREF可通过网络界面（）访问，是分子生态学中的一种新资源，旨在利用高通量测序促进光合真核生物多样性的发现、评估和监测。
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.