Plastid-encoded gene comparison reveals usefulness of atpB, psaA, and rbcL for identification and phylogeny of plastid-containing cryptophyte clades

REFERENCES

• Adolf J.E., Bachvaroff T. & Place A.R. 2008. Can cryptophyte abundance trigger toxic Karlodinium veneficum blooms in eutrophic estuaries? Harmful Algae 8: 119–128. DOI: 10.1016/j.hal.2008.08.003.
   Web of Science ®Google Scholar
• Alppeltans W., Ahyong S.T., Anderseon G., Angel M.V., Artois T., Bailly N., Bamber R., Barber A., Bartsch I., Berta A., et al. 2012. The magnitude of global marine species diversity. Current Biology 22: 2189–2202. DOI: 10.1016/j.cub.2012.09.036.
   Web of Science ®Google Scholar
• Buma A.G.J., Gieskes W.W.C. & Thomses H.A. 1992. Abundance of Cryptophyceae and chlorophyll b-containing organisms in the Weddell-Scotia confluence area in the spring 1988. Polar Biology 12: 43–52. DOI: 10.1007/978-3-642-77595-6_5.
   Web of Science ®Google Scholar
• Choi B., Son M., Kim J.I. & Shin W. 2013. Taxonomy and phylogeny of the genus Cryptomonas (Cryptophyceae, Cryptophyta) from Korea. Algae 28: 307–330. DOI: 10.4490/algae.2013.28.4.307.
   Web of Science ®Google Scholar
• De Vargas C., Audic S., Henry N., Decelle J., Mahé F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., et al. 2015. Eukaryotic plankton diversity in the sunlit ocean. Science 348: 1261605. DOI: 10.1126/science.1261605.
   PubMed Web of Science ®Google Scholar
• Deane J.A., Strachan I.M., Saunders G.W., Hill D.R.A. & McFadden G.I. 2002. Cryptomonad evolution: nuclear 18S rDNA phylogeny versus cell morphology and pigmentation. Journal of Phycology 38: 1236–1244. DOI: 10.1046/j.1529-8817.2002.01250.x.
   Web of Science ®Google Scholar
• Di Tommaso P., Moretti S., Xenarios I., Orobitg M., Montanyola A., Chang J.-M., Taly J.-F. & Notredame C. 2011. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Research 39: W13–W17. DOI: 10.1093/nar/gkr245.
   PubMed Web of Science ®Google Scholar
• Donaher N., Tanifuji G., Onodera N.T., Malfatti S.A., Chain P.S.G., Hara Y. & Archibald J.M. 2009. The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biology and Evolution 1: 439–448. DOI: 10.1093/gbe/evp047.
   PubMed Web of Science ®Google Scholar
• Douglas S.E. & Penny S.L. 1999. The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. Journal of Molecular Evolution 48: 236–244. DOI: 10.1007/PL00006462.
   PubMed Web of Science ®Google Scholar
• Gameiro C., Cartaxana P. & Cabrita M.T. 2004. Variability in chlorophyll and phytoplankton composition in an estuarine system. Hydrobiologia 525: 113–124. DOI: 10.1023/B:HYDR.000.
   Web of Science ®Google Scholar
• Gieskes W.W.C. & Kraay G.W. 1983. Dominance of Cryptophyceae during the phytoplankton spring bloom in the central North Sea detected by HPLC analysis of pigments. Marine Biology 75: 179–185. DOI: 10.1007/BF00406000.
   Web of Science ®Google Scholar
• Guillard R.R.L. & Ryther J.H. 1962. Studies of marine planktonic diatoms: I. Cyclotella nana Hustedt, and Detonula confervaceae (Cleve) Gran. Canadian Journal of Microbiology 8: 229–239. DOI: 10.1139/m62-029.
   PubMed Web of Science ®Google Scholar
• Guiry M.D. & Guiry G.M. 2019. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. http://www.algaebase.org; searched on 01 June 2019.
   Google Scholar
• Hamilton M., Hennon G.M.M., Morales R., Needoba J., Peterson T.D., Schatz M., Swalwell J., Armbrust E.V. & Ribalet F. 2017. Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary. Journal of Plankton Research 39: 589–599. DOI: 10.1093/plankt/fbx029.
   Web of Science ®Google Scholar
• Herfort L., Peterson T.D., McCue L.A., Crump B.C., Prahl F.G., Baptista A.M., Campbell V., Warnick R., Selby M., Roegner G.C. et al. 2011. Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquatic Microbial Ecology 62: 85–97. DOI: 10.3354/ame01460.
   Web of Science ®Google Scholar
• Hoef-Emden K. 2007. Revision of the genus Cryptomonas (Cryptophyceae) II: incongruences between the classical morphospecies concept and molecular phylogeny in smaller pyrenoid-less cells. Phycologia 46: 402–428. DOI: 10.2216/06-83.1.
   Web of Science ®Google Scholar
• Hoef-Emden K. 2008. Molecular phylogeny of phycocyanin-containing cryptophytes: evolution of biliproteins and geographical distribution. Journal of Phycology 44: 985–993. DOI: 10.1111/j.1529-8817.2008.00530.x.
   PubMed Web of Science ®Google Scholar
• Hoef-Emden K. 2012. Pitfalls of establishing DNA barcoding systems in protists: the Cryptophyceae as a test case. PLoS ONE 7: e43652. DOI: 10.1371/journal.pone.0043652.
   PubMed Web of Science ®Google Scholar
• Hoef-Emden K. & Archibald J.M. 2017. Cryptophyta (cryptomonads). In: Handbook of the Protists (Ed. by J.M. Archibald, A.G.B. Simpson, C. Slamovits, L. Margulis, M. Melkonian, D.J. Chapman & J.O. Corliss), pp. 851–891. Springer, Cham. DOI: 10.1007/978-3-319-28149-0_35.
   Google Scholar
• Hoef-Emden K., Marin B. & Melkonian M. 2002. Nuclear and nucleomorph SSU rDNA phylogeny in the Cryptophyta and the evolution of cryptophyte diversity. Journal of Molecular Evolution 55: 161–179. DOI: 10.1007/s00239-002-2313-5.
   PubMed Web of Science ®Google Scholar
• Hoef-Emden K. & Melkonian M. 2003. Revision of the genus Cryptomonas (Cryptophyceae): a combination of molecular phylogeny and morphology provides insights into a long-hidden dimorphism. Protist 154: 371–409. DOI: 10.1078/143446103322454130.
   PubMed Web of Science ®Google Scholar
• Hoef-Emden K., Tran H.-D. & Melkonian M. 2005. Lineage-specific variations of congruent evolution among DNA sequences from three genomes, and relaxed selective constraints on rbcL in Cryptomonas (Cryptophyceae). BMC Evolutionary Biology 5: 56. DOI: 10.1186/1471-2148-5-56.
   PubMed Web of Science ®Google Scholar
• Khan H., Parks N., Kozera C., Curtis B.A., Parsons B.J., Bowman S. & Archibald J.M. 2007. Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Molecular Biology and Evolution 24: 1832–1842. DOI: 10.1093/molbev/msm101.
   PubMed Web of Science ®Google Scholar
• Kim E. & Archibald J.M. 2013. Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist 164: 160–182. DOI: 10.1016/j.protis.2012.10.002.
   Web of Science ®Google Scholar
• Kim J.I., Moore C.E., Archbald J.M., Bhattacharya D., Yi G., Yoon H.S. & Shin W. 2017. Evolutionary dynamics of cryptophytes plastid genomes. Genome Biology and Evolution 9: 1859–1872. DOI: 10.1093/gbe/evx123.
   PubMed Web of Science ®Google Scholar
• Kim J.I., Yoon H.S., Yi G., Kim H.S., Yih W. & Shin W. 2015. The plastid genome of the cryptomonad Teleaulax amphioxeia. PLoS ONE 10: e0129284. DOI: 10.1371/journal.pone.0129284.
   PubMed Web of Science ®Google Scholar
• Kubiszyn A.M., Piwosz K., Wiktor J.M., Jr & Wiktor J.M. 2014. The effect of inter-annual Atlantic water inflow variability on the planktonic protist community structure in the West Spitsbergen waters during the summer. Journal of Plankton Research 36: 1190–1203. DOI: 10.1093/plankt/fbu044.
   Web of Science ®Google Scholar
• Laza-Martínez A. 2012. Urgorri complanatus gen. et sp. nov. (Cryptophyceae), a red-tide-forming species in brackish waters. Journal of Phycology 48: 423–435. DOI: 10.1111/j.1529-8817.2012.01130.x.
   Web of Science ®Google Scholar
• Librado P. & Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452. DOI: 10.1093/bioinformatics/btp187.
   PubMed Web of Science ®Google Scholar
• Marin B., Klingberg M. & Melkonian M. 1998. Phylogenetic relationships among the Cryptophyta: analyses of nuclear-encoded SSU rRNA sequences support the monophyly of extant plastid-containing lineages. Protist 149: 265–276. DOI: 10.1016/S1434-4610(98)70033-1.
   PubMed Web of Science ®Google Scholar
• Medlin L.K., Piwosz K. & Metfies K. 2017. Uncovering hidden biodiversity in the Cryptophyta: clone library studies at the Helgoland time series site in the southern German Bight identifies the cryptophycean clade potentially responsible for the majority of its genetic diversity during the spring bloom. Vie Et Milieu – Life and Environment 67: 27–32. DOI: 10013/epic.51135.
   Web of Science ®Google Scholar
• Medlin L.K. & Strieben S. 2010. Refining cryptophyte identification: matching cell fixation methods to FISH hybridisation of cryptomonads. Journal of Applied Phycology 22: 725–731. DOI: 10.1007/s10811-010-9512-z.
   Web of Science ®Google Scholar
• Metfies K., Gescher C., Frickenhaus S., Niestroy R., Wichels A., Gerdts G., Knefelkamp B., Wiltshire K. & Medlin L. 2010. Contribution of the class Cryptophyceae to phytoplankton structure in the German Bight. Journal of Phycology 46: 1152–1160. DOI: 10.1111/j.1529-8817.2010.00902.x.
   Web of Science ®Google Scholar
• Metfies K. & Medlin L.K. 2007. Refining cryptophyte identification with DNA-microarrays. Journal of Plankton Research 29: 1071–1075. DOI: 10.1093/plankt/fbm080.
   Web of Science ®Google Scholar
• Nozaki H., Nakada T. & Watanabe S. 2010. Evolutionary origin of Gloeomonas (Volvocales, Chlorophyceae), based on ultrastructure of chloroplasts and molecular phylogeny. Journal of Phycology 46: 195–201. DOI: 10.1111/j.1529-8817.2009.00773.x.
   Web of Science ®Google Scholar
• Piwosz K., Kownacka J., Ameryk A., Zalewski M. & Pernthaler J. 2016. Phenology of cryptomonads and the CRY1 lineage in a coastal brackish lagoon (Vistula Lagoon, Baltic Sea). Journal of Phycology 52: 626–637. DOI: 10.1111/jpy.12424.
   Web of Science ®Google Scholar
• Smith D.R. 2012. Updating our view of organelle genome nucleotide landscape. Frontiers in Genetics 3: 175. DOI: 10.3389/fgene.2012.00175.
   Google Scholar
• Stamatakis A. 2014. RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. DOI: 10.1093/bioinformatics/btu033.
   PubMed Web of Science ®Google Scholar
• Swofford D.L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods) Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
   Google Scholar
• Tang K.W., Jakobsen H.H. & Visser A.W. 2001. Phaeocystis globosa (Prymnesiophyceae) and the planktonic food web: feeding, growth, and trophic interactions among grazers. Limnology and Oceanography 46: 1860–1870. DOI: 10.4319/lo.2001.46.8.1860.
   Web of Science ®Google Scholar
• Tanifuji G. & Onodera N.T. 2017. Cryptomonads: a model organism sheds light on the evolutionary history of genome reorganization in secondary endosymbiosis. In: Advances in botanical research, volume 84 secondary endosymbioses (Ed. by Y. Hirakawa), pp. 263–320. Elsevier, Amsterdam. DOI: 10.1016/bs.abr.2017.06.005.
   Google Scholar
• Verbruggen H. & Costa J.F. 2015. The plastid genome of the red alga Laurencia. Journal of Phycology 51: 586–589. DOI: 10.1111/jpy.12297.
   PubMed Web of Science ®Google Scholar
• Yang E.C., Boo G.H., Kim H.J., Cho S.M., Boo S.M., Andersen R.A. & Yoon H.S. 2011. Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles. Protist 163: 217–231. DOI: 10.1016/j.protis.2011.08.001.
   PubMed Web of Science ®Google Scholar
• 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: 21361. DOI: 10.1038/srep21361.
   PubMed Web of Science ®Google Scholar
• Yih W., Kim H.S., Jeong H.J., Myung G. & Kim Y.G. 2004. Ingestion of cryptophyte cells by the marine photosynthetic ciliate Mesodinium rubrum. Aquatic Microbial Ecology 36: 165–170. DOI: 10.3354/ame036165.
   Web of Science ®Google Scholar
• Yoon H.S., Hackett J.D. & Bhattacharya D. 2002. A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proceedings of the National Academy of Scinces of the U.S.A. 99: 11724–11729. DOI: 10.1073/pnas.172234799.
   PubMed Web of Science ®Google Scholar