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High-throughput sequencing for algal systematics

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Pages 256-272 | Received 08 Sep 2017, Accepted 16 Jan 2018, Published online: 18 Apr 2018

References

  • Amaral-Zettler, L.A., Dragone, N.B., Schell, J., Slikas, B., Murphy, L.G., Morrall, C.E. & Zettler, E.R. (2016). Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic. Ecology and Evolution, 7: 516–525.
  • An, S.M., Noh, J.H., Lee, H.R., Choi, D.H., Lee, J.H. & Yang, E.C. (2016). Complete mitochondrial genome of biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae). Mitochondrial DNA Part B, 1: 549–550.
  • Bachvaroff, T.R., Gornik, S.G., Concepcion, G.T., Waller, R.F., Mendez, G.S., Lippmeier, J.C. & Delwiche, C.F. (2014). Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades. Molecular Phylogenetics and Evolution, 70: 314–322.
  • Bakker, F.T. (2017). Herbarium genomics: skimming and plastomics from archival specimens. Webbia: Journal of Plant Taxonomy and Geography, 72: 35–45.
  • Belton, G.S., Prud’homme van Reine, W.F., Huisman, J.M., Draisma, S.G.A. & Gurgel, C.F.D. (2014). Resolving phenotypic plasticity and species designation in the morphologically challenging Caulerpa racemosa–peltata complex (Chlorophyta, Caulerpaceae). Journal of Phycology, 50: 32–54.
  • Beszteri, B., John, U. & Medlin, L.K. (2007). An assessment of cryptic genetic diversity within the Cyclotella meneghiniana species complex (Bacillariophyta) based on nuclear and plastid genes, and amplified fragment length polymorphisms. European Journal of Phycology, 42: 47–60.
  • Bittner, L., Gobet, A., Audic, S., Romac, S., Egge, E.S., Santini, S., Ogata, H., Probert, I., Edvardsen, B. & de Vargas, C. (2013). Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular Ecology, 22: 87–101.
  • Boo, G.H., Hughey, J.R., Miller, K.A. & Boo, S.M. (2016). Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae. Scientific Reports, 6: 35337.
  • Boucher, F.C., Casazza, G., Szövényi, P. & Conti, E. (2016). Sequence capture using RAD probes clarifies phylogenetic relationships and species boundaries in Primula sect. Auricula. Molecular Phylogenetics and Evolution, 104: 60–72.
  • Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M., Rambaut, A. & Drummond, A.J. (2014). BEAST 2: a software platform for Bayesian evolutionary analysis. PLOS Computational Biology, 10: e1003537.
  • Brown, T. A. & Brown, K. (2011). The technical challenges of biomolecular archaeology. In Biomolecular Archaeology: An Introduction (Brown, T.A. & Brown, K., editors), 136–148. Wiley-Blackwell, Oxford.
  • Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. & RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29: 1917–1932.
  • Caporaso, J., Bittinger, K., Bushman, F., DeSantis, T., Andersen, G. & Knight, R. (2010a). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics, 26: 266–267.
  • Caporaso, J., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F., Costello, E., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J. & Knight, R. (2010b). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7: 335–336.
  • Casiraghi, M., Galimberti, A., Sandionigi, A., Bruno, A. & Labra, M. (2016). Life with or without names. Evolutionary Biology, 43: 582–595.
  • Catchen, J., Hohenlohe, P., Bassham, S., Amores, A. & Cresko, W. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22: 3124–3140.
  • Cavalier-Smith, T., Chao, E.E. & Lewis, R. (2015). Multiple origins of Heliozoa from flagellate ancestors: new cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular Phylogenetics and Evolution, 93: 331–362.
  • Choi, J., Lee, H. & Shipunov, A. (2015). All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality. PeerJ, 3: e1087.
  • Clemente, J.C., Jansson, J. & Valiente, G. (2010). Accurate taxonomic assignment of short pyrosequencing reads. Pacific Symposium on Biocomputing, 15: 3–9.
  • Clemente, J., Jansson, J. & Valiente, G. (2011). Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics, 12: 8.
  • Cooper, A. & Poinar, H.N. (2000). Ancient DNA: do it right or not at all. Science, 289: 1139.
  • Costa, J.F., Lin, S.M., Macaya, E.C., Fernández-García, C. & Verbruggen, H. (2016). Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales. BMC Evolutionary Biology, 16: 205.
  • Costello, M.J. & Wilson, S.P. (2011). Predicting the number of known and unknown species in European seas using rates of description. Global Ecology and Biogeography, 20: 319–330.
  • Cruaud, P., Rasplus, J.-Y., Rodriguez, L.J. & Cruaud, A. (2017). High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy. Scientific Reports, 7: 41948.
  • De Clerck, O., Guiry, M.D., Leliaert, F., Samyn, Y., Verbruggen, H. (2013). Algal taxonomy: a road to nowhere? Journal of Phycology, 49: 215–225.
  • de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horak, A., Jaillon, O., Lima-Mendez, G., Luke, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S.G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M.E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P. & Karsenti, E. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science, 348: 1261605-1/11.
  • del Campo, J., Pombert, J.F., Slapeta, J., Larkum, A. & Keeling, P.J. (2017). The ‘other’ coral symbiont: Ostreobium diversity and distribution. The ISME Journal, 11: 296–299.
  • DeLong, E.F. (2009). The microbial ocean from genomes to biomes. Nature, 459: 200–206.
  • Derelle, R., López-García, P., Timpano, H., Moreira, D. (2016). A phylogenomic framework to study the diversity and evolution of Stramenopiles (=Heterokonts). Molecular Biology and Evolution, 33: 2890–2898.
  • Díaz-Tapia, P., Maggs, C.A., West, J.A. & Verbruggen, H. (2017). Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta). Journal of Phycology, 53: 920–937.
  • Dijk, E., Auger, H., Jaszczyszyn, Y. & Thermes, C. (2014). Ten years of next-generation sequencing technology. Trends in Genetics, 30: 418–426.
  • Drummond, A., Suchard, M., Xie, D. & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29: 1969–1973.
  • Dupuis, J.R., Roe, A.D. & Sperling, F.A.H. (2012). Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology, 21: 4422–4436.
  • Eaton, D. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, 30: 1844–1849.
  • Edgar, R. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32: 1792–1797.
  • Edgar, R. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10: 996–998.
  • Edgar, R., Haas, B., Clemente, J., Quince, C. & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27: 2194–2200.
  • Egge, E.S., Johannessen, T.V., Andersen, T., Eikrem, W., Bittner, L., Larsen, A., Sandaa, R.A. & Edvardsen, B. (2015). Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Molecular Ecology, 24: 3026–3042.
  • English, A., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D.M., Reid, J.G., Worley, K.C. & Gibbs, R.A. (2012). Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS ONE, 7: e47768.
  • Finstermeier, K., Zinner, D., Brameier, M., Meyer, M., Kreuz, E., Hofreiter, M. & Roos, C. (2012). A mitogenomic phylogeny of living primates. PLoS ONE, 8: e69504.
  • Forster, D., Micah, D., Mahé, F., Dolan, J.R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie, J.-M., Decelle, J., Edvardsen, B., Egge, E., Eikrem, W., Gobet, A., Kooistra, W.H.C.F., Logares, R., Massana, R., Montresor, M., Not, F., Ogata, H., Pawlowski, J., Pernice, M.C., Romac, S., Shalchian-Tabrizi, K., Simon, N., Richards, T.A., Santini, S., Sarno, D., Siano, R., Vaulot, D., Wincker, P., Zingone, A., de Vargas, C. & Stoeck, T. (2016). Benthic protists: the under-charted majority. FEMS Microbiology Ecology, 92: fiw120.
  • Fosso, B., Santamaria, M., Marzano, M., Alonso-Alemany, D., Valiente, G., Donvito, G., Monaco, A., Notarangelo, P. & Pesole, G. (2015). BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics, 16: 203.
  • Fraser, C.I., McGaughran, A., Chuah, A. & Waters, J.M. (2016). The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages. Molecular Ecology, 25: 3683–3695.
  • Fučíková, K., Lewis, P.O. & Lewis, L.A. (2014). Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta). Journal of Phycology, 50: 14–25.
  • Gabrielson, P.W. (2008a). Molecular sequencing of Northeast Pacific type material reveals two earlier names for Prionitis lyallii, Prionitis jubata and Prionitis sternbergii, with brief comments on Grateloupia versicolor (Halymeniaceae, Rhodophyta). Phycologia, 47: 89–97.
  • Gabrielson, P.W. (2008b). On the absence of previously reported Japanese and Peruvian species of Prionitis (Halymeniaceae, Rhodophyta) in the northeast Pacific. Phycological Research, 56: 105–114.
  • Glenn, T. (2011). Field guide to next‐generation DNA sequencers. Molecular Ecology Resources, 11: 759–769.
  • Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T.J., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D. & Beckman, K.B. (2016). Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology, 34: 942–949.
  • Goodwin, S., McPherson, J.D. & McCombie, W.R. (2016). Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics, 17: 333–351.
  • Gran‐Stadniczeñko, S., Šupraha, L., Egge, E.D. & Edvardsen, B. (2017). Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy. Journal of Eukaryotic Microbiology, 64: 514–532.
  • Guillemin, M.-L., Contreras-Porcia L., Ramírez M.E., Macaya, E.C., Contador, C.B., Woods, H. Wyatt, C. & Brodie, J. (2016). The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: molecular species delimitation reveals extensive diversity. Molecular Phylogenetics and Evolution, 94: 814–826.
  • Harrison, N. & Kidner, C.A. (2011). Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you? Taxon, 60: 1552–1566.
  • Hayden, H.S., Blomster, J., Maggs, C.A., Silva, P.C., Stanhope, M.J. & Waaland, R. (2003). Linnaeus was right all along: Ulva and Enteromorpha are not distinct genera. European Journal of Phycology, 38: 277–294.
  • Head, S.R., Komori, H.K., LaMere, S.A., Whisenant, T., Van Nieuwerburgh, F., Salomon, D.R. & Ordoukhanian, P. (2014). Library construction for next-generation sequencing: overviews and challenges. Biotechniques, 56: 61–4, 66, 68, passim.
  • Heled, J. & Drummond, A. (2010). Bayesian inference of species trees from multilocus data. Molecular Phylogenetics and Evolution, 27: 570–580.
  • Hernandez-Kantun, J.J., Rindi, F., Adey, W.H., Heesch, S., Peña, V., Le Gall, L. & Gabrielson, P.W. (2015). Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans, and related European species L. hibernicum and L. bathyporum (Corallinales, Rhodophyta). Journal of Phycology, 51: 791–807.
  • Herrera, S. & Shank, T.M. (2016). RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Molecular Phylogenetics and Evolution, 100: 70–79.
  • Hind, K.R., Gabrielson, P.W., Lindstrom, S.C. & Martone, P.T. (2014). Misleading morphologies and the importance of sequencing type specimens for resolving coralline taxonomy (Corallinales, Rhodophyta): Pachyarthron cretaceum is Corallina officinalis. Journal of Phycology, 50: 760–764.
  • Huang, H. & Knowles, L.L. (2016). Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of rad sequences. Systematic Biology, 65: 357–365.
  • Hughey, J.R. & Gabrielson, P.W. (2012). Comment on “Acquiring DNA sequence data from dried archival red algae (Florideophyceae) for the purpose of applying variable names to contemporary genetic species: a critical assessment”. Botany, 90: 1191–1194.
  • Hughey, J.R., Silva, P.C. & Hommersand, M.H. (2001). Solving taxonomic and nomenclatural problems in Pacific Gigartinaceae (Rhodophyta) using DNA from type material. Journal of Phycology, 37: 1091–1109.
  • Hughey, J.R., Silva, P.C. & Hommersand, M.H. (2002). ITS1 sequences of type specimens of Gigartina and Sarcothalia and their significance for the classification of South African Gigartinaceae (Gigartinales, Rhodophyta). European Journal of Phycology, 37: 209–216.
  • Hughey, J.R., Gabrielson, P.W., Rohmer, L., Tortolani, J., Silva, M., Miller, K.A., Young, J.D., Martell, C. & Ruediger, E. (2014). Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes. Scientific Reports, 4: 5113.
  • Hughey, J.R., Hommersand, M.H., Gabrielson, P.W., Miller, K.A. & Fuller, T. (2017). Analysis of the complete plastomes of three species of Membranoptera (Ceramiales, Rhodophyta) from Pacific North America. Journal of Phycology, 53: 32–43.
  • Jackson, C., Salomaki, E.D., Lane, C.E. & Saunders G.W. (2017). Kelp transcriptomes provide robust support for interfamilial relationships and revision of the little known Arthrothamnaceae (Laminariales). Journal of Phycology, 53: 1–6.
  • Jain, M., Olsen, H.E., Paten, B. & Akeson, M. (2016). The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology, 17: 239.
  • Janouškovec, J., Liu, S.-L., Martone, P.T., Carré, W., Leblanc, C., Collén, J. & Keeling, P.J. (2013). Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS ONE, 8: e59001.
  • Janouškovec, J., Gavelis, G.S., Burki, F., Dinh, D., Bachvaroff, T.R., Gornik, S.G., Bright, K.J., Imanian, B., Strom, S.L., Delwiche, C.F., Waller, R.F., Fensome, R.A., Leander, B.S., Rohwer, F.L. & Saldarriaga, J.F. (2017). Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. PNAS, 114: E171–E180.
  • Jeong, H., Lim, J.-M., Park, J., Sim, Y.M., Choi, H.-G., Lee, J. & Jeong, W.-J. (2014). Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B. BMC Genomics, 15: 286.
  • Ješovnik, A., Sosa-Calvo, J., Lloyd, M.W., Branstetter, M.G., Fernández, F. & Shultz, T.R. (2017). Phylogenomic species delimitation and host-symbiont coevolution in the fungus-farming ant genus Sericomyrmex Mayr (Hymenoptera: Formicidae): ultraconserved elements (UCEs) resolve a recent radiation. Systematic Entomology, 42: 523–542.
  • Jones, G. (2017). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology, 74: 447–467.
  • Jones, G., Aydin, Z. & Oxelman, B. (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, 31: 991–998.
  • Kang, S.A., Tice, A.K., Spiegel, F.W., Silberman, J.D., Pánek, T., Čepička, I., Kostka, M., Kosakyan, A., Alcântara, D.M., Roger, A.J., Shadwick, L.L., Smirnov, A., Kudryavstev, A., Lahr, D.J.G. & Brown, M.W. (2017). Between a pod and a hard test: the deep evolution of amoebae. Molecular Biology and Evolution, 34: 2258–2270.
  • Karamitros, T. & Magiorkinis, G. (2015). A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits. Nucleic Acids Research, 43: e152–e152.
  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30: 3059–3066.
  • 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., Mentjies, 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.
  • Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Humbert, J.F. & Bouchez, A. (2013). Next‐generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular Ecology Resources, 13: 607–619.
  • Kim, K., Park, J.-H., Bhattacharya, D. & Yoon, H. (2014). Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology, 64: 333–345.
  • Koren, S., Schatz, M.C., Walenz, B.P., Martin, J., Howard, J.T., Ganapathy, G., Wang, Z., Rasko, D.A., McCombie, W.R., Jarvis, E.D. & Phillippy, A.M. (2012). Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30: 693–700.
  • Leliaert, F., Verbruggen, H., Vanormelingen, P., Steen, F., Zuccarello, G.C. & De Clerck, O. (2014). DNA-based species delimitation in algae. European Journal of Phycology, 49: 179–196.
  • Leliaert, F., Tronholm, A., Lemieux, C., Turmel, M., DePriest, M.S., Bhattacharya, D., Karol, K.G., Fredericq, S., Zechman, F.W. & Lopez-Bautista, J.M. (2016). Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Scientific Reports, 6: 25367.
  • Lemieux, C., Otis, C. & Turmel, M. (2014). Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae. BMC Evolutionary Biology, 14: 211.
  • Lemieux, C., Vincent, A.T., Labarre, A., Otis, C. & Turmel, M. (2015). Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae). BMC Evolutionary Biology, 15: 264.
  • Lemmon, E.M. & Lemmon, A.R. (2013). High-throughput genomic data in systematics and phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 44: 99–121.
  • Lindstrom, S.C., Gabrielson, P.W., Hughey, J.R., Macaya, E.C. & Nelson, W.A. (2015). Sequencing of historic and modern specimens reveals cryptic diversity in Nothogenia (Scinaiaceae, Rhodophyta). Phycologia, 54: 97–108.
  • Llamas, B., Valverde, G., Fehren-Schmitz, L., Weyrich, L.S., Cooper, A. & Haak, W. (2017). From the field to the laboratory: controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. STAR: Science & Technology of Archaeological Research, 3: 1–14.
  • Lopes dos Santos, A.L., Gourvil, P., Tragin, M., Noël, M.H., Decelle, J., Romac, S. & Vaulot, D. (2016). Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. The ISME Journal, 11: 512–528.
  • Lu, J.-M., Zhang, N., Du, X.-Y., Wen, J. & Li, D.-Z. (2015). Chloroplast phylogenomics resolves key relationships in ferns. Journal of Systematics and Evolution, 53: 448–457.
  • Lutz, S., Anesio, A.M., Field, K. & Benning, L.G. (2015). Integrated ‘omics’, targeted metabolite and single-cell analyses of Arctic snow algae functionality and adaptability. Frontiers in Microbiology, 6: 1323.
  • Lutz, S., Anesio, A.M., Raiswell, R., Edwards, A., Newton, R.J., Gill, F. & Benning, L.G. (2016). The biogeography of red snow microbiomes and their role in melting arctic glaciers. Nature Communications, 7: 11968.
  • Ma, P.F., Zhang, Y.X., Zeng, C.X., Guo, Z.H. & Li, D.Z. (2014). Chloroplast phylogenomic analyses resolve deep level relationships of an intractable bamboo tribe Arundinarieae (Poaceae). Systematic Biology, 63: 933–950.
  • Magoč, T. & Salzberg, S. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27: 2957–2963.
  • Malviya, S., Scalco, E., Audic, S., Vincent, F., Veluchamy, A., Poulain, J., Wincker, P., Iudicone, D., de Vargas, C., Bittner, L., Zingone, A. & Bowler, C. (2016). Insights into global diatom distribution and diversity in the world’s ocean. Proceedings of the National Academy of Sciences USA, 113: E1516–E1525.
  • 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.
  • Mardis, E. (2017). DNA sequencing technologies: 2006–2016. Nature Protocols, 12: 213–218.
  • McCormack, J., Hird, S., Zellmer, A., Carstens, B. & Brumfield, R. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66: 526–538.
  • McManus, H.A., Sanchez, D.J. & Karol, K.G. (2017). Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae). Peer J, 17: e3325.
  • Montecinos, A. (2016). Species delineation and hybridization in the brown seaweed Ectocarpus complex. Université Pierre et Marie Curie, Universidad Austral de Chile Sciences, Roscoff.
  • Montecinos, A.E., Couceiro, L., Peters, A.F., Desrut, A., Valero, M. & Guillemin, M.-L. (2017). Species delimitation and phylogeographic analyses in the Ectocarpus subgroup siliculosi (Ectocarpales, Phaeophyceae). Journal of Phycology, 53: 17–31.
  • Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods, 5: 621–628.
  • Muñoz-Gómez, S.A., Mejía-Franco, F.G., Durnin, K., Colp, M., Grisdale, C.J., Archibald, J.M. & Slamovits, C.H. (2017). The new red algal subphylum Proteorhodophytina comprises the largest and most divergent plastid genomes known. Current Biology, 27: 1–8.
  • Nozaki, H., Yamada, T.K., Takahashi, F., Matsuzaki, R. & Nakada, T. (2014). New “missing link” genus of the colonial volvocine green algae gives insights into the evolution of oogamy. BMC Evolutionary Biology, 14: 37.
  • Page, R.D.M. (2016). DNA barcoding and taxonomy: dark taxa and dark texts. Philosophical Transactions of the Royal Society B, 371: 20150334.
  • Parker, J., Helmstetter, A.J., Devey, D., Wilkinson, T. & Papadoupulos, A.S.T. (2017). Field-based species identification of closely-related plants using real-time nanopore sequencing. Scientific Reports, 7: 8345.
  • Parks, D.H., Rinke, C., Chuvochina, M., Chaumeil, P.A., Woodcroft, B.J., Evans, P.N., Hugenholtz, P. & Tyson, G.W. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the Tree of Life. Nature Microbiology, 2: 1533–1542.
  • Payo, D.A., Leliaert, F., Verbruggen, H., D’hondt, S., Calumpong, H.P. & De Clerck, O. (2013). Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines. Proceedings of the Royal Society B: Biological Sciences, 280: 20122660.
  • Prosser, S.W.J., deWaard, J.R., Miller, S.E. & Hebert, P.D.N. (2016). DNA barcodes from century-old type specimens using next-generation sequencing. Molecular Ecology Resources, 16: 487–497.
  • Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M. & Lemmon, A.R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526: 569–573.
  • Rappe, M.S. & Giovannoni, S.J. (2003). The uncultured microbial majority. Annual Review of Microbiology, 57: 369–394.
  • Reuter, J.A., Spacek, D. & Snyder, M.P. (2015). High-throughput sequencing technologies. Molecular Cell, 58: 586–597.
  • Reviers, B. & Rousseau, F. (1999). Towards a new classification of the brown algae. In Progress in Phycology Research (Round, F.E. & Chapman, D.J., editors), 13: 107–201. Biopress Ltd, Bristol.
  • Rhoads, A. & Au, K.F. (2015). PacBio sequencing and its applications. Genomics, Proteomics & Bioinformatics, 13: 278–289.
  • Rittmeyer, E.N. & Austin, C.C. (2015). Combined next-generation sequencing and morphology reveal fine-scale speciation in crocodile skinks (Squamata: Scincidae: Tribolonotus). Molecular Ecology, 24: 466–483.
  • Rubin B.E.R., Ree R.H. & Moreau C.S. (2012). Inferring phylogenies from RAD sequence data. PLoS ONE, 7: 1–12.
  • Ruck, E.C., Nakov, T., Alverson, A.J. & Theriot, E.C. (2016). Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales. Molecular Phylogenetics and Evolution, 103: 155–171.
  • Särkinen, T., Staats, M., Richardson, J.E., Cowan, R.S. & Bakker, F.T. (2012). How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS ONE, 7: e43808.
  • Saunders, G.W. & Kucera, H. (2010). An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Cryptogamie, Algologie, 31: 487–528.
  • Saunders, G.W. & McDevit, D.C. (2012). Acquiring DNA sequence data from dried archival red algae (Florideophyceae) for the purpose of applying available names to contemporary genetic species: a critical assessment. Botany, 90: 191–203.
  • Sauvage, T., Schmidt, W.E., Suda, S. & Fredericq, S. (2016). A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA. BMC Ecology, 16: 8.
  • Schloss, P., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J. & Weber, C.F. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied Environmental Microbiology, 75: 7537–7541.
  • Schmieder, R. & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27: 863–864.
  • Sěvčıková, T., V. Klimeš, V., Zbránková, V., Strnad, H., Hroudová, M., Vlček, C. & Eliáš, M. (2016). A comparative analysis of mitochondrial genomes in Eustigmatophyte algae. Genome Biology and Evolution, 8: 705–722.
  • Sherwood, A.R. & Presting, G.G. (2007). Universal primers amplify a 23S rDNA plastid marker in eukaryotic algae and cyanobacteria. Journal of Phycology, 43: 605–608.
  • Sherwood, A.R., Dittbern, M.N., Johnston, E.T. & Conklin, K.Y. (2016). A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko’olau mountain range on the island of O’ahu, Hawai’i. Journal of Phycology, 53: 437–445.
  • Shokralla, S., Spall, J.L., Gibson, J.F. & Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21: 1794–1805.
  • Shokralla, S., Porter, T.M., Gibson, J.F., Dobosz, R., Janzen, D.H., Hallwachs, W., Golding, G.B. & Hajibabaei, M. (2015). Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports, 5: 9687.
  • Silberfeld, T., Leigh, J.W., Verbruggen, H., Cruaud, C., de Reviers, B. & Rousseau, F. (2010). A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): investigating the evolutionary nature of the “brown algal crown radiation”. Molecular Phylogenetics and Evolution, 56: 659–674.
  • Sissini, M.N., Oliveira, M.C., Gabrielson, P.W., Robinson, N.M., Okolodkov, Y.B., Riosmena-Rodriguez, R. & Horta, P.A. (2014). Mesophyllum erubescens (Corallinales, Rhodophyta) –so many species in one epithet. Phytotaxa, 190: 299–319.
  • Song, H., Lee, J., Graf, L., Rho, M., Qiu, H., Bhattacharya, D. & Yoon, H. (2016). A novice’s guide to analyzing NGS-derived organelle and metagenome data. Algae, 31: 137–154.
  • Song, S., Zhao, J. & Li, C. (2017). Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences. Molecular Phylogenetics and Evolution, 111: 44–55.
  • Staats, M., Erkens, R.H.J., van de Vossenberg, B., Wieringa, J.J., Kraaijeveld, K., Stielow, B., Geml, J., Richardson, J.E. & Bakker, F.T. (2013). Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PLoS ONE, 8: e69189.
  • Steven, B., McCann, S. & Ward, N.L. (2012). Pyrosequencing of plastid 23S rRNA genes reveals diverse and dynamic cyanobacterial and algal populations in two eutrophic lakes. FEMS Microbiology Ecology, 82: 607–615.
  • Sun, J., Wang, L., Wu, S., Wang, X., Xiao, J., Chi, S., Liu, C., Ren, L., Zhao, Y., Liu, T. & Yu, J. (2014). Transcriptome-wide evolutionary analysis on essential brown algae (Phaeophyceae) in China. Acta Oceanologica Sinica, 33: 13–19.
  • Suzuki, M., Segawa, T., Mori, H., Akiyoshi, A., Ootsuki, R., Kurihara, A., Sakayama, H., Kitayama, T., Abe, T., Kogame, K., Kawai, H. & Nozaki, H. (2016). Next-generation sequencing of an 88-year-old specimen of the poorly known species Liagora japonica (Nemaliales, Rhodophyta) supports the recognition of Otohimella gen. nov. PLoS ONE, 11: 1–18.
  • Verbruggen, H. (2014). Morphological complexity, plasticity, and species diagnosability in the application of old species names in DNA-based taxonomies. Journal of Phycology, 50: 26–31.
  • Verbruggen, H., Ashworth, M., LoDuca, S.T., Vlaeminck, C., Cocquyt, E., Sauvage, T., Zechman, F.W., Littler, D.S., Littler, M.M., Leliaert, F. & De Clerck, O. (2009). A multi-locus time-calibrated phylogeny of the siphonous green algae. Molecular Phylogenetics and Evolution, 50: 642–653.
  • Verbruggen, H., Maggs, C.A., Saunders, G.W., Le Gall, L., Yoon, H.S. & De Clerck, O. (2010). Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evolutionary Biology, 10: 16.
  • Verbruggen, H., Marcelino, V.R., Guiry, M.D., Cremen, Ma. C.M. & Jackson, C.J. (2017). Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data. Journal of Phycology, 53: 790–803.
  • Vieira, C., Camacho, O., Wynne, M.J., Mattio, L., Anderson R.J., Bolton, J.J., Sanson, M., D’Hondt, S., Leliaert, F., Fredericq, S., Payri, C. & De Clerck, O. (2016). Shedding new light on old algae: matching names and sequences in the brown algal genus Lobophora (Dictyotales, Phaeophyceae). Taxon, 65: 689–707.
  • Villain, A., Kojadinovic, M., Puppo, C., Prioretti, L., Hubert, P., Zhang, Y., Grégori, G., Roulet, A., Roques, C., Claverie, J.-M., Gontero, B. & Blanc, G. (2017). Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. Mitochondrial DNA Part B, 2: 97–98.
  • Wang, L., Mao, Y., Kong, F., Li, G., Ma, F., Zhang, B., Sun, P., Bi, G., Zhang, F., Xue, H. & Cao, M. (2013). Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis. PLoS ONE 8: e65902.
  • Worden, A.Z., Janouskovec, J., McRose, D., Engman, A., Welsh, R.M., Malfatti, S., Tringe, S.G. & Keeling, P.J. (2012). Global distribution of a wild alga revealed by targeted metagenomics. Current Biology, 22: 675–677.
  • Yang, E.C., Kim, K.M., Kim, S.Y., Lee, J.M., Boo, G.H., Lee, J.-H., Nelson, W.A., Yi, G., Schmidt, W.E., Fredericq, S., Boo, S.M., Bhattacharya, D. & Yoon, H.S. (2015). Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biology Evolution, 7: 2394–2406.
  • Yang, E.C., Boo, S.M., Bhattacharya, D., Saunders, G.W., Knoll, A.H., Fredericq, S., Graf, L. & Yoon, H.S. (2016). Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Scientific Reports, 6: 2136.
  • Yang, Z. & Rannala, B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Phylogenetics and Evolution, 31: 3125–3135.
  • Yeates, D.K., Zwick, A. & Mikheyev, A.S. (2016). Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world’s biological collections. Current Opinion in Insect Science, 18: 83–88.
  • Zhang, L., Wang, X., Liu, T., Wang, H., Wang, G., Chi, S. & Liu, C. (2015). Complete plastid genome of the brown alga Costaria costata (Laminariales, Phaeophyceae). PLoS ONE, 10: e0140144.

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