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

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A Correction to this article was published on 06 July 2021

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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 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.

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Data Availability

The whole genome assembly was deposited into the NCBI/GenBank Whole Genome Sequence (WGS) database with the accession number JAALGZ000000000 and raw genomic reads into NCBI/Short Read Archive (SRA) with accession numbers SRR12496087 and SRR12496088, all of which are under the BioProject PRJNA607370. The mitochondrial genome was deposited into the NCBI/GenBank database with the accession number MT267870. Data S1 and S2 are available via Mendeley Data at DOI: https://doi.org/10.17632/cg2ys63ps2.1.

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Acknowledgments

This research utilized computational resources and services provided by the National Computational Infrastructure (NCI), which is supported by the Australian Government. We thank Samuel Lysy for his assistance in the lab. We would also like to thank Robert Ruge of Deakin University for assistance and use of the SIT HPC Cluster.

Funding

Funding for this study was provided by the Mary Collins Trust and the Deakin Genomics Centre, Deakin University (Australia).

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Authors and Affiliations

  1. Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia

    Mun Hua Tan, Stella Loke, Laurence J. Croft & Stacey M. Trevathan-Tackett

  2. Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia

    Mun Hua Tan, Stella Loke & Laurence J. Croft

  3. School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia

    Mun Hua Tan

  4. Department of Microbiology and Immunology, University of Melbourne, Bio21 Institute, Melbourne, Victoria, Australia

    Mun Hua Tan

  5. School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia

    Frank H. Gleason

  6. BioEconomy, Research & Advisory, Valby, Copenhagen, Denmark

    Lene Lange

  7. Protein Chemistry and Enzyme Technology, Department of Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark

    Bo Pilgaard

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  1. Mun Hua Tan
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Contributions

STT, SL, MT, LC, LL, and FHG designed the research and direction of analyses. STT collected and isolated the sample. SL performed whole genome and transcriptome sequencing. MT assembled and annotated the genome and transcriptome, and carried out phylogenetic analysis. LC and MT performed comparative analyses of assemblies and proteomes of other protist genomes. LL, BP, and MT analyzed the peptide-based functional annotation of CAZymes. MT and STT led the writing of the manuscript. All authors edited and developed the manuscript.

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Correspondence to Stacey M. Trevathan-Tackett.

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The original online version of this article was revised: The supplementary materials contained errors.

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Tan, M.H., Loke, S., Croft, L.J. et al. First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation. Microb Ecol 82, 498–511 (2021). https://doi.org/10.1007/s00248-020-01647-x

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