title: Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes.
abstract: Labyrinthulomycetes are heterotrophic stramenopiles that are ubiquitous in a wide range of both marine and freshwater habitats and play important roles in decomposition of organic matter. The diversity and taxonomy of Labyrinthulomycetes has been studied for many years, but we nevertheless lack both a comprehensive reference database and up-to-date phylogeny including all known diversity, which hinders many global insights into their ecological distribution and the relative importance of various subgroups in different environments. Here, we present a curated reference database and a phylogenetic tree of Labyrinthulomycetes small subunit ribosomal RNA (SSU or 18S rRNA) data. Based on this created reference database, we analyzed high-throughput environmental sequencing data, revealing many previously unknown environmental clades and exploring the ecological distribution of various subgroups. Particularly, a number of newly identified environmental clades that are widespread in the open ocean. Comparing the manually curated reference database to existing tools for identification of environmental sequences (e.g. PR2 or SILVA databases) suggests that the curated database provides a higher degree of specificity and a lower frequency of misidentification. The phylogenetic framework and database will be a useful tool for future ecological and evolutionary studies.
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Jingwen
authors.initials: J
authors.lastname: Pan
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Javier
authors.initials: J
authors.lastname: Del Campo
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D004275:DNA, Ribosomal / Q000235:genetics; D030561:Databases, Nucleic Acid; D004777:Environment; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009792:Oceans and Seas; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA; D058009:Stramenopiles / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: 18s rRNA; amphitremids; high-throughput sequencing; labyrinthulids; phylogeny; thraustochytrids