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Tan MH, Loke S, Croft LJ, Gleason FH, Lange L, Pilgaard B, Trevathan-Tackett SM. First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation. MICROBIAL ECOLOGY 2021; 82:498-511. [PMID: 33410934 DOI: 10.1007/s00248-020-01647-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
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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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Bio21 Institute, Melbourne, Victoria, Australia
| | - Stella Loke
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Laurence J Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Frank H Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lene Lange
- BioEconomy, Research & Advisory, Valby, Copenhagen, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stacey M Trevathan-Tackett
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.
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Menning DM, Gravley HA, Cady MN, Pepin D, Wyllie-Echeverria S, Ward DH, Talbot SL. Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.62823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north Pacific, we leveraged metabarcoding of environmental DNA extracted from water, sediment, and eelgrass tissue samples collected from five widely distributed eelgrass meadows in Alaska and one in Japan and uncovered wide prevalence of two classes of pathogenic organisms – Labyrinthula zosterae and other associated strains of Labyrinthula, and the Phytophthora/Halophytophthora blight species complex – known to have caused decline in eelgrass (Zostera marina) elsewhere in the species’ global distribution. Although the distribution of these disease organisms is not well understood in the north Pacific, we uncovered the presence of at least one eelgrass pathogen at every locality sampled.
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