PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution
PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution
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DOI：
10.1111/1755-0998.12410
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发表时间：
2015-11-01
影响因子：
7.7
通讯作者：
de Vargas, Colomban
中科院分区：
文献类型：
--
作者：
Morard, Raphael;Darling, Kate F.;de Vargas, Colomban
浮游有孔虫（根虫）是普遍存在的海洋中上层原生生物，产生具有明显形态的钙质壳。它们在海洋碳循环中发挥着重要作用，它们独特的化石记录是生物年代地层学和过去气候重建的基础。在过去的二十年里，一项主要的全球采样工作已经建立了多个大型的低温保存的浮游有孔虫个体样本集合。已生成了数千个18S rDNA部分序列，代表了世界范围内所有已知的主要形态分类群。这种全面的数据覆盖提供了一个机会，以整体的方式评估整个浮游原生生物群体的分子生态学和进化模式。我们结合了所有已发表和未发表的遗传数据，建立了PFR2，即浮游有孔虫核糖体参考数据库。第一版数据库包括从460个海洋站点收集的现存浮游有孔虫的47个已知形态种中的32个的3322个参考18S rDNA序列。所有的序列都经过严格的分类整理，使用一个完全解析到形态物种水平的六级注释系统，并链接到一系列元数据。PFR2网站可在以下网址下载整个数据库或特定部分，以及识别新的浮游有孔虫序列。其新颖，充分记录策展过程整合了形态学和分子分类学的进步。它允许增加其分类分辨率，并通过包括对注释的完整意外跟踪和确保注释在内部保持一致来确保完整性。
Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR2, the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR2 website, available at , allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.