| [1] | Kirkham AR, Lepère C, Jardillier LE, Not F, Bouman H, Mead A, et al. A global perspective on marine photosynthetic picoeukaryote community structure. ISME J. 2013;7: 922–936. doi: 10.1038/ismej.2012.166. pmid:23364354
|
| [2] | Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: Integrating terrestrial and oceanic components. Science. 1998;281: 237–240. pmid:9657713 doi: 10.1126/science.281.5374.237
|
| [3] | Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12: e1001889. doi: 10.1371/journal.pbio.1001889. pmid:24959919
|
| [4] | Medlin LK, Sáez AG, Young JR. A molecular clock for coccolithophores and implications for selectivity of phytoplankton extinctions across the K/T boundary. Mar Micropaleontol. 2008;67: 69–86. doi: 10.1016/j.marmicro.2007.08.007
|
| [5] | Shiraiwa Y. Physiological regulation of carbon fixation in the photosynthesis and calcification of coccolithophorids. Comp Biochem Physiol B Biochem Mol Biol. 2003;136: 775–783. pmid:14662302 doi: 10.1016/s1096-4959(03)00221-5
|
| [6] | Li C, Yang G, Pan J, Zhang H. Experimental studies on dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) production by four marine microalgae. Acta Oceanol Sin. 2010;29: 78–87. doi: 10.1007/s13131-010-0052-9
|
| [7] | John U, Beszteri S, Gl？ckner G, Singh R, Medlin L, Cembella AD. Genomic characterisation of the ichthyotoxic prymnesiophyte Chrysochromulina polylepis, and the expression of polyketide synthase genes in synchronized cultures. Eur J Phycol. 2010;45: 215–229. doi: 10.1080/09670261003746193
|
| [8] | Alderkamp A-C, Buma AGJ, Rijssel van M. The carbohydrates of Phaeocystis and their degradation in the microbial food web. In: Leeuwe MA van, Stefels J, Belviso S, Lancelot C, Verity PG, Gieskes WWC, editors. Phaeocystis, major link in the biogeochemical cycling of climate-relevant elements. Springer Netherlands; 2007. pp. 99–118.
|
| [9] | Hemaiswarya S, Raja R, Kumar RR, Ganesan V, Anbazhagan C. Microalgae: a sustainable feed source for aquaculture. World J Microbiol Biotechnol. 2011;27: 1737–1746. doi: 10.1007/s11274-010-0632-z
|
| [10] | Simon M, López-García P, Moreira D, Jardillier L. New haptophyte lineages and multiple independent colonizations of freshwater ecosystems. Environ Microbiol Rep. 2013;5: 322–332. doi: 10.1111/1758-2229.12023. pmid:23584973
|
| [11] | Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, et al. Diversity patterns of uncultured haptophytes unravelled by pyrosequencing in Naples Bay. Mol Ecol. 2013;22: 87–101. doi: 10.1111/mec.12108. pmid:23163508
|
| [12] | Liu H, Probert I, Uitz J, Claustre H, Aris-Brosou S, Frada M, et al. Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proc Natl Acad Sci U S A. 2009;106: 12803–12808. doi: 10.1073/pnas.0905841106. pmid:19622724
|
| [13] | Shalchian-Tabrizi K, Reier-R？berg K, Ree DK, Klaveness D, Br？te J. Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences. J Eukaryot Microbiol. 2011;58: 315–318. doi: 10.1111/j.1550-7408.2011.00547.x. pmid:21518078
|
| [14] | Jones HLJ, Leadbeater BSC, Green JC. Mixotrophy in haptophytes. The Haptophyte Algae. Oxford: Clarendon Press; 1994. pp. 247–264.
|
| [15] | Edvardsen B, Eikrem W, Throndsen J, Sáez AG, Probert I, Medlin LK. Ribosomal DNA phylogenies and a morphological revision provide the basis for a revised taxonomy of the Prymnesiales (Haptophyta). Eur J Phycol. 2011;46: 202–228. doi: 10.1080/09670262.2011.594095
|
| [16] | Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature. 2013;499: 209–213. doi: 10.1038/nature12221. pmid:23760476
|
| [17] | Marsh ME. Regulation of CaCO3 formation in coccolithophores. Comp Biochem Physiol B Biochem Mol Biol. 2003;136: 743–754. pmid:14662299 doi: 10.1016/s1096-4959(03)00180-5
|
| [18] | Holligan PM, Viollier M, Harbour DS, Camus P, Champagne-Philippe M. Satellite and ship studies of coccolithophore production along a continental shelf edge. Nature. 1983;304: 339–342. doi: 10.1038/304339a0
|
| [19] | Von Dassow P, John U, Ogata H, Probert I, Bendif EM, Kegel JU, et al. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. ISME J. 2014. doi: 10.1038/ismej.2014.221
|
| [20] | McDonald S., Sarno D, Scanlan D., Zingone A. Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle. Aquat Microb Ecol. 2007;50: 75–89. doi: 10.3354/ame01148
|
| [21] | Egge ES, Eikrem W, Edvardsen B. Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. J Eukaryot Microbiol. 2015;62: 121–140. doi: 10.1111/jeu.12157. pmid:25099994
|
| [22] | Bigelow N, Barker J, Ryken S, Patterson J, Hardin W, Barlow S, et al. Chrysochromulina sp.: A proposed lipid standard for the algal biofuel industry and its application to diverse taxa for screening lipid content. Algal Res. 2013;2: 385–393. doi: 10.1016/j.algal.2013.07.001
|
| [23] | Jordan RW, Chamberlain AHL. Biodiversity among haptophyte algae. Biodivers Conserv. 1997;6: 131–152.
|
| [24] | Stiller JW, Schreiber J, Yue J, Guo H, Ding Q, Huang J. The evolution of photosynthesis in chromist algae through serial endosymbioses. Nat Commun. 2014;5. doi: 10.1038/ncomms6764
|
| [25] | Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, et al. The tree of eukaryotes. Trends Ecol Evol. 2005;20: 670–676. pmid:16701456 doi: 10.1016/j.tree.2005.09.005
|
| [26] | Wang D, Ning K, Li J, Hu J, Han D, Wang H, et al. Nannochloropsis genomes reveal evolution of microalgal oleaginous traits. PLoS Genet. 2014;10: e1004094. doi: 10.1371/journal.pgen.1004094. pmid:24415958
|
| [27] | Vaulot D, Birrien J-L, Marie D, Casotti R, Veldhuis MJW, Kraay GW, et al. Morphology, ploidy, pigment composition, and genome size of cultured strains of Phaeocystis (prymnesiophyceae). J Phycol. 1994;30: 1022–1035. doi: 10.1111/j.0022-3646.1994.01022.x
|
| [28] | Green JC, Course PA, Tarran GA. The life-cycle of Emiliania huxleyi: A brief review and a study of relative ploidy levels analysed by flow cytometry. J Mar Syst. 1996;9: 33–44. doi: 10.1016/0924-7963(96)00014-0
|
| [29] | Hunsperger HM, Randhawa T, Cattolico RA. Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae. BMC Evol Biol. 2015;15: 16. doi: 10.1186/s12862-015-0286-4. pmid:25887237
|
| [30] | Hovde BT, Starkenburg SR, Hunsperger HM, Mercer LD, Deodato CR, Jha RK, et al. The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. BMC Genomics. 2014;15: 604. doi: 10.1186/1471-2164-15-604. pmid:25034814
|
| [31] | Guo Z, Zhang H, Lin S. Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina. PloS One. 2014;9: e114941. doi: 10.1371/journal.pone.0114941. pmid:25506945
|
| [32] | Padilla GM. Genetic expression in the cell cycle. Elsevier; 2012. doi: 10.1016/b978-0-12-543720-2.50005-8
|
| [33] | Sforza E, Simionato D, Giacometti GM, Bertucco A, Morosinotto T. Adjusted light and dark cycles can optimize photosynthetic efficiency in algae growing in photobioreactors. PLoS ONE. 2012;7. doi: 10.1371/journal.pone.0038975
|
| [34] | Ragni M, D’Alcala M. Circadian variability in the photobiology of Phaeodactylum tricornutum: pigment content. J Plankton Res. 2007; 141–156. doi: 10.1093/plankt/fbm002
|
| [35] | Rost B, Riebesell U, Sültemeyer D. Carbon acquisition of marine phytoplankton: Effect of photoperiod length. Limnol Oceanogr. 2006;51: 12–20. doi: 10.4319/lo.2006.51.1.0012
|
| [36] | Trentacoste EM, Shrestha RP, Smith SR, Glé C, Hartmann AC, Hildebrand M, et al. Metabolic engineering of lipid catabolism increases microalgal lipid accumulation without compromising growth. Proc Natl Acad Sci U S A. 2013;110: 19748–19753. doi: 10.1073/pnas.1309299110. pmid:24248374
|
| [37] | Radakovits R, Jinkerson RE, Darzins A, Posewitz MC. Genetic engineering of algae for enhanced biofuel production. Eukaryot Cell. 2010;9: 486–501. doi: 10.1128/EC.00364-09. pmid:20139239
|
| [38] | Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, Seibert M, et al. Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J Cell Mol Biol. 2008;54: 621–639. doi: 10.1111/j.1365-313x.2008.03492.x
|
| [39] | Jeffery SW, Brown MR, Volkman JK. Haptophytes as feedstocks in mariculture. The Haptophyte Algae. Oxford: Clarendon Press; 1994. pp. 287–302.
|
| [40] | Lee S, Seo CH, Lim B, Yang JO, Oh J, Kim M, et al. Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucleic Acids Res. 2011;39: e9. doi: 10.1093/nar/gkq1015. pmid:21059678
|
| [41] | Bigelow NW, Hardin WR, Barker JP, Ryken SA, Macrae AC, Cattolico RA. A comprehensive GC-MS sub-microscale assay for fatty acids and its applications. J Am Oil Chem Soc. 2011;88: 1329–1338. pmid:21909157 doi: 10.1007/s11746-011-1799-7
|
| [42] | Manning SR, La Claire JW. Prymnesins: Toxic metabolites of the golden alga, Prymnesium parvum Carter (Haptophyta). Mar Drugs. 2010;8: 678–704. doi: 10.3390/md8030678. pmid:20411121
|
| [43] | Staunton J, Weissman KJ. Polyketide biosynthesis: a millennium review. Nat Prod Rep. 2001;18: 380–416. pmid:11548049 doi: 10.1039/a909079g
|
| [44] | Shen B. Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Curr Opin Chem Biol. 2003;7: 285–295. pmid:12714063 doi: 10.1016/s1367-5931(03)00020-6
|
| [45] | Etchegaray A, Rabello E, Dieckmann R, Moon DH, Fiore MF, D？hren von H, et al. Algicide production by the filamentous cyanobacterium Fischerella sp. CENA 19. J Appl Phycol. 2004;16: 237–243. doi: 10.1023/B:JAPH.0000048509.77816.5e.
|
| [46] | Finking R, Marahiel MA. Biosynthesis of nonribosomal peptides. Annu Rev Microbiol. 2004;58: 453–488. pmid:15487945 doi: 10.1146/annurev.micro.58.030603.123615
|
| [47] | Du L, Sánchez C, Shen B. Hybrid peptide-polyketide natural products: biosynthesis and prospects toward engineering novel molecules. Metab Eng. 2001;3: 78–95. pmid:11162234 doi: 10.1006/mben.2000.0171
|
| [48] | Aron ZD, Dorrestein PC, Blackhall JR, Kelleher NL, Walsh CT. Characterization of a new tailoring domain in polyketide biogenesis: the amine transferase domain of MycA in the mycosubtilin gene cluster. J Am Chem Soc. 2005;127: 14986–14987. pmid:16248612 doi: 10.1021/ja055247g
|
| [49] | Fisch KM. Biosynthesis of natural products by microbial iterative hybrid PKS–NRPS. RSC Adv. 2013;3: 18228–18247. doi: 10.1039/c3ra42661k
|
| [50] | Sondergaard TE, Hansen FT, Purup S, Nielsen AK, Bonefeld-J？rgensen EC, Giese H, et al. Fusarin C acts like an estrogenic agonist and stimulates breast cancer cells in vitro. Toxicol Lett. 2011;205: 116–121. doi: 10.1016/j.toxlet.2011.05.1029. pmid:21683775
|
| [51] | Gelderblom WC, Thiel PG, Jaskiewicz K, Marasas WF. Investigations on the carcinogenicity of fusarin C—a mutagenic metabolite of Fusarium moniliforme. Carcinogenesis. 1986;7: 1899–1901. pmid:2876785 doi: 10.1093/carcin/7.11.1899
|
| [52] | Maiya S, Grundmann A, Li X, Li S-M, Turner G. Identification of a hybrid PKS/NRPS required for pseurotin A biosynthesis in the human pathogen Aspergillus fumigatus. Chembiochem Eur J Chem Biol. 2007;8: 1736–1743. doi: 10.1002/cbic.200700202
|
| [53] | Masschelein J, Mattheus W, Gao L-J, Moons P, Van Houdt R, Uytterhoeven B, et al. A PKS/NRPS/FAS hybrid gene cluster from Serratia plymuthica RVH1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics. PloS One. 2013;8: e54143. doi: 10.1371/journal.pone.0054143. pmid:23349809
|
| [54] | Hamilton-Miller JM. Chemistry and biology of the polyene macrolide antibiotics. Bacteriol Rev. 1973;37: 166–196. pmid:4202146
|
| [55] | Fouces R, Mellado E, Díez B, Barredo JL. The tylosin biosynthetic cluster from Streptomyces fradiae: genetic organization of the left region. Microbiol Read Engl. 1999;145 (Pt 4): 855–868. doi: 10.1099/13500872-145-4-855
|
| [56] | Cundliffe E, Bate N, Butler A, Fish S, Gandecha A, Merson-Davies L. The tylosin-biosynthetic genes of Streptomyces fradiae. Antonie Van Leeuwenhoek. 2001;79: 229–234. pmid:11816964 doi: 10.1023/a:1012065300116
|
| [57] | Baltz RH, Seno ET, Stonesifer J, Wild GM. Biosynthesis of the macrolide antibiotic tylosin. A preferred pathway from tylactone to tylosin. J Antibiot (Tokyo). 1983;36: 131–141. doi: 10.7164/antibiotics.36.131
|
| [58] | Morar M, Pengelly K, Koteva K, Wright GD. Mechanism and diversity of the erythromycin esterase family of enzymes. Biochemistry (Mosc). 2012;51: 1740–1751. doi: 10.1021/bi201790u
|
| [59] | Miura K, Ueno S, Kamiya K, Kobayashi J, Matsuoka H, Ando K, et al. Cloning of mRNA sequences for two antibacterial peptides in a hemipteran insect, Riptortus clavatus. Zoolog Sci. 1996;13: 111–117. pmid:8688805 doi: 10.2108/zsj.13.111
|
| [60] | Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S. CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res. 2010;38: D774–780. doi: 10.1093/nar/gkp1021. pmid:19923233
|
| [61] | Torrent M, Nogués MV, Boix E. Discovering new in silico tools for antimicrobial peptide prediction. Curr Drug Targets. 2012;13: 1148–1157. pmid:22664076 doi: 10.2174/138945012802002311
|
| [62] | Sims JJ, Donnell MS, Leary JV, Lacy GH. Antimicrobial agents from marine algae. Antimicrob Agents Chemother. 1975;7: 320–321. pmid:1137385 doi: 10.1128/aac.7.3.320
|
| [63] | Al-Saif SSA, Abdel-Raouf N, El-Wazanani HA, Aref IA. Antibacterial substances from marine algae isolated from Jeddah coast of Red sea, Saudi Arabia. Saudi J Biol Sci. 2014;21: 57–64. doi: 10.1016/j.sjbs.2013.06.001. pmid:24596500
|
| [64] | Sun X, Gilroy EM, Chini A, Nurmberg PL, Hein I, Lacomme C, et al. ADS1 encodes a MATE-transporter that negatively regulates plant disease resistance. New Phytol. 2011;192: 471–482. doi: 10.1111/j.1469-8137.2011.03820.x. pmid:21762165
|
| [65] | Jin Y, Nair A, van Veen HW. Multidrug transport protein norM from Vibrio cholerae simultaneously couples to sodium- and proton-motive force. J Biol Chem. 2014;289: 14624–14632. doi: 10.1074/jbc.M113.546770. pmid:24711447
|
| [66] | Omote H, Hiasa M, Matsumoto T, Otsuka M, Moriyama Y. The MATE proteins as fundamental transporters of metabolic and xenobiotic organic cations. Trends Pharmacol Sci. 2006;27: 587–593. pmid:16996621 doi: 10.1016/j.tips.2006.09.001
|
| [67] | Eckardt NA. Move it on out with MATEs. Plant Cell. 2001;13: 1477–1480. pmid:11449044 doi: 10.1105/tpc.13.7.1477
|
| [68] | Rodríguez-Beltrán J, Rodríguez-Rojas A, Guelfo JR, Couce A, Blázquez J. The Escherichia coli SOS gene dinF protects against oxidative stress and bile salts. PloS One. 2012;7: e34791. doi: 10.1371/journal.pone.0034791. pmid:22523558
|
| [69] | Slamovits CH, Okamoto N, Burri L, James ER, Keeling PJ. A bacterial proteorhodopsin proton pump in marine eukaryotes. Nat Commun. 2011;2: 183. doi: 10.1038/ncomms1188. pmid:21304512
|
| [70] | Kazamia E, Czesnick H, Nguyen TTV, Croft MT, Sherwood E, Sasso S, et al. Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation. Environ Microbiol. 2012;14: 1466–1476. doi: 10.1111/j.1462-2920.2012.02733.x. pmid:22463064
|
| [71] | Ruiz-González MX, Marín I. New insights into the evolutionary history of type 1 rhodopsins. J Mol Evol. 2004;58: 348–358. pmid:15045490 doi: 10.1007/s00239-003-2557-8
|
| [72] | Bamann C, Bamberg E, Wachtveitl J, Glaubitz C. Proteorhodopsin. Biochim Biophys Acta. 2014;1837: 614–625. doi: 10.1016/j.bbabio.2013.09.010. pmid:24060527
|
| [73] | Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, et al. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PloS One. 2013;8: e57487. doi: 10.1371/journal.pone.0057487. pmid:23526944
|
| [74] | Béjà O, Lanyi JK. Nature’s toolkit for microbial rhodopsin ion pumps. Proc Natl Acad Sci U S A. 2014;111: 6538–6539. doi: 10.1073/pnas.1405093111. pmid:24737891
|
| [75] | Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, et al. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc Natl Acad Sci U S A. 2008;105: 16561–16565. doi: 10.1073/pnas.0807162105. pmid:18922772
|
| [76] | Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, et al. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci U S A. 2005;102: 18147–18152. pmid:16330755 doi: 10.1073/pnas.0509073102
|
| [77] | Shand RF, Betlach MC. Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light. J Bacteriol. 1991;173: 4692–4699. pmid:1856168
|
| [78] | Sharma AK, Spudich JL, Doolittle WF. Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol. 2006;14: 463–469. pmid:17008099 doi: 10.1016/j.tim.2006.09.006
|
| [79] | Wisecaver JH, Hackett JD. Dinoflagellate genome evolution. Annu Rev Microbiol. 2011;65: 369–387. doi: 10.1146/annurev-micro-090110-102841. pmid:21682644
|
| [80] | Tabita FR, Hanson TE, Li H, Satagopan S, Singh J, Chan S. Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev MMBR. 2007;71: 576–599. pmid:18063718 doi: 10.1128/mmbr.00015-07
|
| [81] | Boczar BA, Delaney TP, Cattolico RA. Gene for the ribulose-1,5-bisphosphate carboxylase small subunit protein of the marine chromophyte Olisthodiscus luteus is similar to that of a chemoautotrophic bacterium. Proc Natl Acad Sci U S A. 1989;86: 4996–4999. pmid:2740337 doi: 10.1073/pnas.86.13.4996
|
| [82] | Newman SM, Cattolico RA. Structural, functional, and evolutionary analysis of ribulose-1,5-bisphosphate carboxylase from the chromophytic alga Olisthodiscus luteus. Plant Physiol. 1987;84: 483–490. pmid:16665466 doi: 10.1104/pp.84.2.483
|
| [83] | Portis AR. Rubisco activase—Rubisco’s catalytic chaperone. Photosynth Res. 2003;75: 11–27. pmid:16245090
|
| [84] | Maier UG, Fraunholz M, Zauner S, Penny S, Douglas S. A nucleomorph-encoded CbbX and the phylogeny of RuBisCo regulators. Mol Biol Evol. 2000;17: 576–583. pmid:10742049 doi: 10.1093/oxfordjournals.molbev.a026337
|
| [85] | Zarzycki J, Axen SD, Kinney JN, Kerfeld CA. Cyanobacterial-based approaches to improving photosynthesis in plants. J Exp Bot. 2013;64: 787–798. doi: 10.1093/jxb/ers294. pmid:23095996
|
| [86] | Fujita K, Tanaka K, Sadaie Y, Ohta N. Functional analysis of the plastid and nuclear encoded CbbX proteins of Cyanidioschyzon merolae. Genes Genet Syst. 2008;83: 135–142. pmid:18506097 doi: 10.1266/ggs.83.135
|
| [87] | Starkenburg SR, Kwon KJ, Jha RK, McKay C, Jacobs M, Chertkov O, et al. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics. 2014;15: 212. doi: 10.1186/1471-2164-15-212. pmid:24646409
|
| [88] | Mueller-Cajar O, Stotz M, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M. Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase. Nature. 2011;479: 194–199. doi: 10.1038/nature10568. pmid:22048315
|
| [89] | Whitney SM, Houtz RL, Alonso H. Advancing our understanding and capacity to engineer nature’s CO2-sequestering enzyme, Rubisco. Plant Physiol. 2011;155: 27–35. doi: 10.1104/pp.110.164814. pmid:20974895
|
| [90] | Helliwell KE, Wheeler GL, Leptos KC, Goldstein RE, Smith AG. Insights into the evolution of vitamin B12 auxotrophy from sequenced algal genomes. Mol Biol Evol. 2011;28: 2921–2933. doi: 10.1093/molbev/msr124. pmid:21551270
|
| [91] | Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature. 2005;438: 90–93. pmid:16267554 doi: 10.1038/nature04056
|
| [92] | Koid AE, Liu Z, Terrado R, Jones AC, Caron DA, Heidelberg KB. Comparative transcriptome analysis of four prymnesiophyte algae. PloS One. 2014;9: e97801. doi: 10.1371/journal.pone.0097801. pmid:24926657
|
| [93] | Oudot-Le Secq M-P, Green BR. Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Gene. 2011;476: 20–26. doi: 10.1016/j.gene.2011.02.001. pmid:21320580
|
| [94] | Kim E, Lane CE, Curtis BA, Kozera C, Bowman S, Archibald JM. Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics. 2008;9: 215. doi: 10.1186/1471-2164-9-215. pmid:18474103
|
| [95] | Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18: 821–829. doi: 10.1101/gr.074492.107. pmid:18349386
|
| [96] | Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12: 491. doi: 10.1186/1471-2105-12-491. pmid:22192575
|
| [97] | Smit A, Hubley, R, Green, P. RepeatMasker Open-3.0 [Internet]. 2010.
|
| [98] | Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinforma Oxf Engl. 2009;25: 1105–1111. doi: 10.1093/bioinformatics/btp120
|
| [99] | Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28: 511–515. doi: 10.1038/nbt.1621. pmid:20436464
|
| [100] | Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinforma Oxf Engl. 2007;23: 1061–1067. doi: 10.1093/bioinformatics/btm071
|
| [101] | Stanke M, Sch？ffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006;7: 62. pmid:16469098 doi: 10.1186/1471-2105-7-62
|
| [102] | Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5: 59. pmid:15144565 doi: 10.1186/1471-2105-5-59
|
| [103] | Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008;18: 1979–1990. doi: 10.1101/gr.081612.108. pmid:18757608
|
| [104] | Conesa A, G？tz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinforma Oxf Engl. 2005;21: 3674–3676. doi: 10.1093/bioinformatics/bti610
|
| [105] | Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, et al. Manipulation of FASTQ data with Galaxy. Bioinforma Oxf Engl. 2010;26: 1783–1785. doi: 10.1093/bioinformatics/btq281
|
| [106] | Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5: 621–628. doi: 10.1038/nmeth.1226. pmid:18516045
|
| [107] | Raivo Kolde. pheatmap: Pretty Heatmaps. R package [Internet].
|
| [108] | Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29: 644–652. doi: 10.1038/nbt.1883. pmid:21572440
|
| [109] | Jochem FJ. Dark survival strategies in marine phytoplankton assessed by cytometric measurement of metabolic activity with fluorescein diacetate. Mar Biol. 1999;135: 721–728. doi: 10.1007/s002270050673
|
| [110] | Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 2009;77 Suppl 9: 89–99. doi: 10.1002/prot.22540. pmid:19701941
|
| [111] | Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, et al. Chapter nineteen—Rosetta3: an object-oriented software suite for the simulation and design of macromolecules. In: Michael L. Johnson and Ludwig Brand, editor. Methods in Enzymology. Academic Press; 2011. pp. 545–574. doi: 10.1016/B978-0-12-381270-4.00019-6. pmid:21187238
|
| [112] | O’Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, et al. A combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput. 2015. doi: 10.1021/ct500864r
|
| [113] | Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292: 195–202. pmid:10493868 doi: 10.1006/jmbi.1999.3091
|
| [114] | Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004;32: W526–W531. pmid:15215442 doi: 10.1093/nar/gkh468
|
| [115] | Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminformatics. 2012;4: 17. doi: 10.1186/1758-2946-4-17
|
| [116] | Rohl CA, Strauss CEM, Misura KMS, Baker D. Protein structure prediction using Rosetta. Methods Enzymol. 2004;383: 66–93. pmid:15063647 doi: 10.1016/s0076-6879(04)83004-0
|
| [117] | Davis IW, Baker D. RosettaLigand Docking with Full Ligand and Receptor Flexibility. J Mol Biol. 2009;385: 381–392. doi: 10.1016/j.jmb.2008.11.010. pmid:19041878
|
| [118] | Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. pmid:15034147 doi: 10.1093/nar/gkh340
|
| [119] | Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinforma Oxf Engl. 2005;21: 2104–2105. doi: 10.1093/bioinformatics/bti263
|
| [120] | Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008;25: 1253–1256. doi: 10.1093/molbev/msn083. pmid:18397919
|
| [121] | Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19: 1572–1574. pmid:12912839 doi: 10.1093/bioinformatics/btg180
|
| [122] | Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29: 1969–1973. doi: 10.1093/molbev/mss075. pmid:22367748
|
| [123] | Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22: 2688–2690. pmid:16928733 doi: 10.1093/bioinformatics/btl446
|
