High-throughput sequencing of the kelp Alaria (Phaeophyceae) reveals epi-endobiotic associations, including a likely phaeophycean parasite

References

• Assis, J., Araújo, M.B. & Serrão, E.Á. (2018). Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic. Global Change Biology, 24: e55–e66.
   Google Scholar
• Beck, N. & Lang, B. (2010). MFannot, organelle genome annotation webserver. http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl.
   Google Scholar
• Bella, J., Bao, Y., Gloor, G., Burton, J. & Reid, G. (2013). High throughput sequencing methods and analysis for microbiome research. Journal of Microbiological Methods, 95: 401–414. https://doi.org/10.1016/j.mimet.2013.08.011
   Google Scholar
• Bjærke, M.R. & Fredriksen, S. (2003). Epiphytic macroalgae on the introduced brown seaweed Sargassum muticum (Yendo) Fensholt (Phaeophyceae) in Norway. Sarsia North Atlantic Marine Science, 88: 353–364.
   Google Scholar
• Bringloe, T.T., Starko, S., Wade, R.M., Vieira, C., Kawai, H., Clerck, O., Cock, J.M., Coelho, S.M., Destombe, C., Valero, M., Neiva, J., Pearson, G.A., Faugeron, S., Serrão, E.A. & Verbruggen, H. (2020). Phylogeny and evolution of the brown algae. Critical Reviews in Plant Sciences, 39: 281–321.
   Web of Science ®Google Scholar
• Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17: 540–552.
   Google Scholar
• Cremen, M.C.M., Huisman, J.M., Marcelino, V.R. & Verbruggen, H. (2016). Taxonomic revision of Halimeda (Bryopsidales, Chlorophyta) in south-western Australia. Australian Systematic Botany, 29: 41–54.
   Google Scholar
• Delmont, T.O., Gaia, M., Hinsinger, D.D., Fremont, P., Guerra, A.F., Eren, A.M., Vanni, C., Kourlaiev, A., d’Agata, L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Dilva, C., Wessner, M., Noel, B., Aury, J-M., Tara Oceans Coordinators, de Vargas, C., Bowler, C., Karsenti, E., Pelletier, E., Wincker, P. & Jaillon, O. (2020). Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics. bioRxiv: https://doi.org/10.1101/2020.10.15.341214.
   Google Scholar
• Deshmukhe, G.V. & Tatewaki, M. (2001). Phenology of brown alga Coilodesme japonica (Phaeophyta, Dictyosiphonales) with respect to the host-specificity along Muroran coast, North Pacific Ocean, Japan. Indian Journal of Marine Science, 30: 161–165.
   Google Scholar
• Dierckxsens, N., Mardulyn, P. & Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data, Nucleic Acids Research, 45: e18.
   Google Scholar
• Fuller, P.L., Knott, D.M., Kingsley-Smith, P.R., Morris, J.A., Buckel, C.A., Hunter, M.E. & Hartman, L.D. (2014). Invasion of Asian tiger shrimp, Penaues monodon Fabricius, 1798, in the western north Atlantic and Gulf of Mexico. Aquatic Invasions, 9: 59–70.
   Google Scholar
• Gauna, M.C., Cáceres, E.J. and Parodi, E.R. (2015). Spatial and temporal variability in algal epiphytes on Patagonian Dictyota dichotoma (Dictyotales, Phaeophyceae). Aquatic Botany, 120: 338–345.
   Google Scholar
• Hardy, S.M., Carr, C.M., Hardmann, M., Steinke, D., Corstorphine, E. & Mah, C. (2010). Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools. Marine Biodiversity, 41: 195–210.
   Google Scholar
• Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B, 270: 313–321.
   Google Scholar
• Heesch, S., & Peters, A.F. (1999). Scanning electron microscopy observation of host entry by two brown algae endolithic in Laminaria saccharina (Laminariales, Phaeophyceae). Phycological Research, 47: 1–5.
   Google Scholar
• Heesch, S., Peters, A.F., Broom, J.E. & Hurd, C.L. (2008). Affiliation of the parasite Herpodiscus durvillaeae (Phaeophyceae) with the Sphacelariales based on DNA sequence comparisons and morphological observations. European Journal of Phycology, 43: 283–295.
   Google Scholar
• Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. & Drummond, A. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28: 1647–1649.
   Google Scholar
• Klochkova, T.A., Klimova, A.V. & Klochkova, N.G. (2018). Infraspecies forms of Alaria esculenta (Laminariales, Ochrophyta) in the marine flora of Eastern Kamchatka: first revision. Bulletin оf Kamchatka State Technical University, 43: 74–86.
   Google Scholar
• Knauf, U. & Hachtel, W. (2002). The genes encoding subunits of ATP synthases are conserved in the reduced plastid genomes of the heterotrophic alga Prototheca wickerhamii. Molecular Genetics and Genomics, 267: 492–497.
   Google Scholar
• Kraan, S. (2020). Concise review of the genus Alaria Greville, 1830. Journal of Applied Phycology. https://doi.org/10.1007/s10811-020-02222-0.
   Google Scholar
• Kuckuck, P. (1955). Ectocarpaceen-Studien III Protectocarpus nov. gen. Helgoländer wissenschaftliche Meeresuntersuchungen, 5: 119–140.
   Google Scholar
• Langmead, B. & Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9: 357–359.
   Google Scholar
• Le Gall, L. & Saunders, G.W. (2010). DNA barcoding is a powerful tool to uncover algal diversity: a case study of the Phyllophoraceae (Gigartinales, Rhodophyta) in the Canadian flora. Journal of Phycology, 46: 374–389.
   Google Scholar
• Leray, M. & Knowlton, N. (2014). DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences USA, 112: 2076–2081.
   Google Scholar
• Liu, F., Zhang, Y., Bi, Y., Chen, W. & Moejes, F.W. (2018). Understanding the evolution of mitochondrial genomes in Phaeophyceae inferred from mitogenome of Ishige okamurae (Ishigeales) and Dictyopteris divaricata (Dictyotales). Journal of Molecular Evolution, 87: 16–26.
   Google Scholar
• Marcelino, V.R., & Verbruggen, H. (2016). Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae. Scientific Reports, 6: 31508.
   PubMed Web of Science ®Google Scholar
• Murúa, P., Küpper, F.C., Muñoz, L.A., Bernard, M. & Peters, A.F. (2018). Microspongium alariae in Alaria esculenta: a widely-distributed non-parasitic brown algal endophyte that shows cell modifications within its host. Botanica Marina, 61: 343–354.
   Google Scholar
• Nurk, S., Bankevich, A., Antipov, D., Gurevich, A., Korobeynikov, A., Lapidus, A., Prjibelsky, A., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepenauskas, R., McLean, J., Lasken, R., Clingenpeel, S.R., Woyke, T., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2013). Assembling genomes and mini-metagenomes from highly chimeric reads. In Research in Computational Molecular Biology (Deng, M., Jiang, R., Sun, F. & Zhang, X., editors). Springer, Berlin.
   Google Scholar
• Oliveira, M.C., Repetti, S.I., Iha, C., Jackson, C.J., Díaz-Tapia, P., Lubiana, K.M.F., Cassano, V., Costa, J.F., Cremen, M.C.M., Marcelino, V.R. & Verbruggen, H. (2018). High-throughput sequencing for algal systematics. European Journal of Phycology, 53: 256–272.
   Google Scholar
• Pedersen, P.M. (1981). Culture studies on the rare brown alga Phaeostroma longisetum comb. nov. and its common relative P. pustulosum from Greenland. Nordic Journal of Botany, 1: 271–276.
   Google Scholar
• Pedersen, P.M. (2011). Grønlands havalger. Epsilon.dk. (In Danish.)
   Google Scholar
• Preuss, M., Verbruggen, H. & Zuccarello, G.C. (2020). The organelle genomes in the photosynthetic red algal parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) have elevated substitution rate and extreme gene loss in the plastid genome. Journal of Phycology, 56: 1006–1018.
   Google Scholar
• Qiu, Z., Coleman, M.A., Provost, E., Campbell, A.H., Kelaher, B.P., Dalton, S.J., Thomas, T., Steinberg, P.D. & Marzinelli, E.M. (2019). Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp. Proceedings of the Royal Society B: Biological Sciences, 286: 20181887.
   Google Scholar
• Ratnasingham, S. & Hebert, P.D.N. (2013). A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE, 8: e66312.
   Google Scholar
• Rodríguez, G. & Suárez, H. (2001). Anthropogenic dispersal of decapod crustaceans in aquatic environments. Interciencia, 26: 282–288.
   Web of Science ®Google Scholar
• Ronowicz, M., Wlodarska-Kowalczuk, M. & Kuklinski, P. (2008). Factors influencing hydroids (Cnidaria: Hydrozoa) biodiversity and distribution in arctic kelp forest. Journal of Marine Biological Association of the United Kingdom, 88: 1567–1575.
   Google Scholar
• Round, F.E., Crawford, R.M. & Mann, D.G. (1990). The Diatoms: Biology and Morphology of the Genera. Cambridge University Press, New York.
   Google Scholar
• Ryberg, M. & Nilsson, R.H. (2018). New light on names and naming of dark taxa. MycoKeys, 30: 31–39.
   Web of Science ®Google Scholar
• Salomaki, E.D., Nickles, K.R. & Lane, C.E. (2015). The ghost plastid of Choreocolax polysiphoniae. Journal of Phycology, 51: 217–221.
   Google Scholar
• Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30: 1312–1313.
   Google Scholar
• Starko, S., Bringloe, T.T., Gomez, M.S., Darby, H., Graham, S.W., Martone, P.T. (in review). Genomic rearrangements and sequence evolution across brown algal organelles.
   Google Scholar
• Stekoll, M.S. (2019). The seaweed resources of Alaska. Botanica Marina, 62: 227–235.
   Web of Science ®Google Scholar
• Tanaka, N. (1986). Adhesive strength of epiphytic diatoms on various seaweeds. Bulletin of the Japanese Society of Scientific Fisheries, 52: 817–821.
   Google Scholar
• Tragin, M. & Vaulot, D. (2019). Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. Scientific Reports, 9: 5190.
   Google Scholar
• Tyler-Walters, H. (2003). A hydroid (Obelia longissima). In Marine Life Information Network: Biology and Sensitivity Key Information Reviews (Tyler-Walters, H. & Hiscock, K., editors). Plymouth: Marine Biological Association of the United Kingdom.
   Google Scholar
• Van der Loos, L.M., Eriksson, B.K. & Salles, J.F. (2019). The macroalgal holobiont in a changing sea. Trends in Microbiology, 27: 635–650.
   Google Scholar
• Wertheim, J.O., Murrell, B., Smith, M.D., Pond, S.L.K. & Scheffler, K. (2015). RELAX: detecting relaxed selection in a phylogenetic framework. Molecular Biology and Evolution, 32: 820–832.
   Google Scholar
• Wlodarska-Kowalczuk, M., Kuklinski, P., Ronowicz, M., Legezynska, J. & Gromisz, S. (2009). Assessing species richness of macrofauna associated with macroalgae in Arctic kelp forests (Hornsund, Svalbard). Polar Biology, 32: 897–905.
   Google Scholar
• Zerbino, D.R. & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821–829.
   Google Scholar