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

Abstract

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 virulence and ecology. Given these uncertainties, we investigated Labyrinthula from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate of 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'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 specialised substrate affinity and the scarcity of characterised 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 ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between Labyrinthula species and its host substrate.

Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics

“…2021, Tan et al. 2021). It has been hypothesized that poor representation of specific organisms can account for lower than expected shared single‐copy orthologs which has been seen in multiple cultured Stramenopiles (Hackl et al.…”

Method Development Progress in Genetic Engineering of Thraustochytrids

“…Most eukaryotic microorganisms have not been identified to date, and among those known to have biotechnologically interesting properties, only a small fraction have been transformed. This review compiles the current knowledge that is either used or have the potential to be used in one group of marine microorganisms that, evolutionarily, is quite different from other organisms as recently shown [ 122 ]. However, the approaches and elements used are similar to those used in other species, such as yeast, green microalgae, and diatoms, and hence will be relevant to consider for eukaryotic microorganisms in general.…”

Standard ecological and molecular research methods and techniques for Labyrinthula spp.

“…Many techniques have been utilized to study the biology of Labyrinthula in the laboratory, including culture-based isolation, molecular and morphological characterization, pathogenicity assays, transmission dynamics, host immunity responses, fatty acid analyses, microscopy, and virulence. More recently, emerging research on host immunity (Duffin et al, 2020), discovery of Labyrinthula's role in primary DHA production (Kumon et al, 2002;Yoshioka et al, 2019) and the recent sequencing of the first Labyrinthula genome (Tan et al, 2021) have highlighted the importance and potential for advancement of discoveries related to this unique protist.…”

“…sequencing (Tan et al, 2021) and success in developing prototypic genetic-level species delineations (Martin et al, 2016), there are new opportunities to resolve historic and ongoing discoveries into speciation and evolution of Labyrinthula.…”

“…The first whole genome for Labyrinthula has been assembled and published, sourced from axenic culture from southeast Australia (Tan et al, 2021) and previously identified within the pathogenic clade and confirmed via pathogen testing (Martin et al, 2016;Trevathan-Tackett et al, 2018a). The first genome and transcriptome provide novel insight into Labyrinthula phylogeny and an opportunity to explore the genes available and used by Labyrinthula.…”