First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation

• Published in: Microbial ecology 2021-08, Vol.82 (2), p.498-511
• Main Authors: Tan, Mun Hua, Loke, Stella, Croft, Laurence J., Gleason, Frank H., Lange, Lene, Pilgaard, Bo, Trevathan-Tackett, Stacey M.
• Format: Article
• Language: English
• Subjects: Actin; Annotations; Biomedical and Life Sciences; Carbohydrates; Catalysts; Degradation; Ecology; Enzymes; Evolutionary genetics; Genes and Genomes; Genomes; Geoecology/Natural Processes; Labyrinthula; Life Sciences; Marine ecology; Microbial Ecology; Microbiology; Molecular interactions; Myosin; Nature Conservation; Opportunist infection; Parasites; Pathogens; Phylogeny; Probability theory; Proteins; Proteomes; Protists; Sea grasses; Seagrasses; Storage; Substrate preferences; Substrates; Virulence; Water Quality/Water Pollution
• ISSN: 0095-3628; 1432-184X
• DOI: 10.1007/s00248-020-01647-x

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C’s actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.