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.

Differential Gene Expression in Five Isolates of the Clam Pathogen, Quahog Parasite Unknown (QPX)

“…; Pan et al. ). The transcriptomes of these five isolates, herein considered to represent the same species, were then profiled with a specific focus on exploring the potential molecular basis for virulence differences among QPX isolates and for possible genetic adaptations to local environmental conditions.…”

“…Five QPX isolates were investigated including three isolates with previously sequenced and nearly identical full length small subunit (SSU) RNA gene and two new QPX isolates for which SSU gene sequences were obtained during preliminary assays (Table 1, Data S1). The similarity of almost full length SSU gene sequences from these five isolates (pairwise identity: 99.32-99.94%) suggests that the isolates are most likely the same species considering that 3-5% difference in the SSU gene is typically used as a threshold to designate species within the Labyrinthulomycetes (Mo et al 2002;Pan et al 2016). The transcriptomes of these five isolates, herein considered to represent the same species, were then profiled with a specific focus on exploring the potential molecular basis for virulence differences among QPX isolates and for possible genetic adaptations to local environmental conditions.…”

Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches

“…arguably at the genus level or above). Our reference phylogenetic tree can be therefore considered as a useful tool to approach new ecological and evolutionary questions (Pan et al, 2017) and classify the unknown sequences (Mahé et al, 2017) like it has already been done for other groups of eukaryotic microorganisms (del Campo et al, 2018).…”

Not in your usual Top 10: protists that infect plants and algae

“…Labyrinthula spp. are protists in the Labyrinthulida (Stramenopila), and are phylogenetically basal to oomycetes (Pan et al, 2017;Tsui et al, 2009). High-throughput environmental DNA sampling, ITS and ribosomal sequences suggest that Labyrinthula spp.…”

“…High-throughput environmental DNA sampling, ITS and ribosomal sequences suggest that Labyrinthula spp. are highly diverse, and globally distributed (Bockelmann et al, 2013;Collado-Mercado et al, 2010;Martin et al, 2016;Pan et al, 2017). These organisms are saline tolerant, and can be saprobes, coral inhabitants, endosymbionts of amoebae or endophytic facultative parasites of marine and terrestrial plants (Amon, 1978;Bigelow et al, 2005;Pan et al, 2017;Sullivan et al, 2013).…”