DOI: 10.5061/dryad.6cj8h
title: Data from: A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA

description: Background: In spite of their ecological importance as primary producers
 and microbioeroders of marine calcium carbonate (CaCO3) substrata,
 endolithic phototrophs spanning both prokaryotic (the cyanobacteria) and
 eukaryotic algae lack established molecular resources for their
 facilitated survey with high throughput sequencing. Here, the development
 of a metabarcoding framework for the elongation factor EF-Ttu (tufA) was
 tested on four Illumina-sequenced marine CaCO3 microfloras for the
 characterization of their endolithic phototrophs, especially the abundant
 bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel
 tufA degenerate primers and a comprehensive database enabling Operational
 Taxonomic Unit (OTU) identification at multiple taxonomic ranks with
 percent identity thresholds determined herein. Results: The newly
 established tufA database comprises 4057 non-redundant sequences (from
 1339 eukaryotic and prokaryotic phototrophs, and 2718 prokaryotic
 heterotrophs) including 27 classes in 10 phyla of phototrophic diversity
 summarized from data mining on GenBank®, our barcoding of &gt;150
 clones produced from coral reef microfloras, and &gt;300 eukaryotic
 phototrophs (&gt;230 Ulvophyceae including &gt;100 ‘Ostreobium’
 spp., and &gt;70 Florideophyceae, Phaeophyceae and miscellaneous
 taxa). Illumina metabarcoding with the newly designed primers resulted in
 802 robust OTUs including 618 phototrophs and 184 heterotrophs (77 and 23
 % of OTUs, respectively). Phototrophic OTUs belonged to 14 classes of
 phototrophs found in seven phyla, and represented ~98 % of all reads. The
 phylogenetic profiles of coral reef microfloras showed few OTUs in large
 abundance (proportion of reads) for the Chlorophyta (Ulvophyceae, i.e.
 Ostreobium and Phaeophila), the Rhodophyta (Florideophyceae) and
 Haptophyta (Coccolithophyceae), and a large diversity (richness) of OTUs
 in lower abundance for the Cyanophyta (Cyanophyceae) and the Ochrophyta
 (the diatoms, ‘Bacillariophyta’). The bioerosive ‘Ostreobium’ spp.
 represented four families in a large clade of subordinal divergence, i.e.
 the Ostreobidineae, and a fifth, phylogenetically remote family in the
 suborder Halimedineae (provisionally assigned as the
 ‘Pseudostreobiaceae’). Together they harbor 85–95 delimited cryptic
 species of endolithic microsiphons. Conclusions: The novel degenerate
 primers allowed for amplification of endolithic phototrophs across a wide
 phylogenetic breadth as well as their recovery in very large proportions
 of reads (overall 98 %) and diversity (overall 77 % of OTUs). The
 established companion tufA database and determined identity thresholds
 allow for OTU identification at multiple taxonomic ranks to facilitate the
 monitoring of phototrophic assemblages via metabarcoding, especially
 endolithic communities rich in bioeroding Ulvophyceae, such as those
 harboring ‘Ostreobium’ spp., Phaeophila spp. and associated algal
 diversity.
description: tufA
 databaseTufA database for OTU
 annotation (sequences span the length of the metabarcode, i.e. the second
 half of tufA). Annotation consists of fields separated by '|'
 and include Genbank Accession, Category (Phototroph, Heterotroph), Domain,
 Phylum, Class, Order, Family and Genus.tufADB_metabarcoding_BMC2016_accession_category_domain_phylum_class_order_family_genus.fasAnnotated OTUs (Phototrophs)Annotated Core OTUs clustered with UPARSE and SWARM. Annotation are found in fields separated by '|' and include OTU number, Domain, Phylum, Class, Order, Family and Genus.OTUs_phototrophs_UPARSE_SWARM_BMC2016_number_domain_phylum_class_order_family_genus.fas