Abstract
Cyanobacteria are a widespread and important bacterial phylum, responsible for a significant portion of global carbon and nitrogen fixation. Unfortunately, reliable and accurate automated classification of cyanobacterial 16S rRNA gene sequences is muddled by conflicting systematic frameworks, inconsistent taxonomic definitions (including the phylum itself), and database errors. To address this, we introduce Cydrasil 3 (https://www.cydrasil.org), a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification. Cydrasil 3 contains over 1300 manually curated sequences longer than 1100 base pairs and can be used for phylogenetic placement or as a reference sequence set for de novo phylogenetic reconstructions. The web application (utilizing PaPaRA and EPA-ng) can place thousands of sequences into the reference tree and has detailed instructions on how to analyze results. While the Cydrasil web application offers no taxonomic assignments, it instead provides phylogenetic placement, as well as a searchable database with curation notes and metadata, and a mechanism for community feedback.
Highlights
Background & SummaryCyanobacteria are oxygenic photosynthetic microorganisms, widespread in both terrestrial and marine ecosystems[1,2] that sustain many ecosystem services including carbon[3] and nitrogen fixation[4]
The rise of high-throughput DNA sequencing, development of easy to use analysis pipelines[5,6] and availability of comprehensive biodiversity databases has simplified molecular microbial surveys, including those focused on abundance and diversity of cyanobacteria
Errors in the two most used databases, Silva[7] and Greengenes[8], which are well documented[9,10,11], lead to recurrent taxonomic misassignments. Though this uncertainty can be viewed as a trade-off for both efficiency and coverage, it becomes amplified when examining cyanobacteria, due to the complex history of cyanobacterial systematics
Summary
Cyanobacteria are oxygenic photosynthetic microorganisms, widespread in both terrestrial and marine ecosystems[1,2] that sustain many ecosystem services including carbon[3] and nitrogen fixation[4]. Errors in the two most used databases, Silva[7] and Greengenes[8], which are well documented[9,10,11], lead to recurrent taxonomic misassignments Though this uncertainty can be viewed as a trade-off for both efficiency and coverage, it becomes amplified when examining cyanobacteria, due to the complex history of cyanobacterial systematics. In modern amplicon analysis and classification, it is not uncommon for two sequences to be assigned to the same species epithet but be separated by vast phylogenetic distance This problem stems from the practice of delineating new taxa by sequence alignment with a small set of sequences of known organisms most closely related to the one being studied, instead of examining them in the context of a comprehensive phylogeny that would provide a full picture. We envision three common use cases for the Cydrasil reference package: provide a “first look” at the phylogenetic location of a given 16S rRNA cyanobacterial sequence (of any length) within the context of a full phylogenetic reconstruction, alleviate researchers need to spend time collecting sequences for de novo phylogenetic analysis, and act as a reference package for sequence placement algorithms
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