Diversity and evolution of cytochromes P450 in stramenopiles

[1]  Robert D. Finn,et al.  Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species , 2017, Nucleic Acids Res..

[2]  D. Nelson Cytochrome P450 diversity in the tree of life. , 2018, Biochimica et biophysica acta. Proteins and proteomics.

[3]  S. Dittami,et al.  Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica , 2017, Front. Plant Sci..

[4]  T. Mock,et al.  Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species , 2017, Front. Plant Sci..

[5]  G. von Heijne,et al.  Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants , 2017, Molecular biology and evolution.

[6]  D. Richter,et al.  Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome , 2017, eLife.

[7]  O. Gotoh,et al.  Evolutionary origin of mitochondrial cytochrome P450 , 2017, Journal of biochemistry.

[8]  Lieven Sterck,et al.  Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. , 2017, The New phytologist.

[9]  E. Corre,et al.  Herbivore-induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata , 2017, PloS one.

[10]  L. Mukhtarova,et al.  Epoxyalcohol synthase of Ectocarpus siliculosus. First CYP74-related enzyme of oxylipin biosynthesis in brown algae. , 2017, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[11]  Vincent Moulton,et al.  Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus , 2017, Nature.

[12]  Takayuki Tohge,et al.  Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism , 2016, Nature Communications.

[13]  J. Tuszynski,et al.  Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s , 2016, Scientific Reports.

[14]  N. Satoh,et al.  A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[15]  S. Karpov,et al.  Heterokont Predator Develorapax marinus gen. et sp. nov. – A Model of the Ochrophyte Ancestor , 2016, Front. Microbiol..

[16]  N. Baliga,et al.  Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. , 2016, Marine genomics.

[17]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[18]  S. O’Brien,et al.  Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds , 2016, Genome biology and evolution.

[19]  Zhen Li,et al.  Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN] , 2016, Plant Cell.

[20]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[21]  D. Nelson,et al.  Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes , 2015, Scientific Reports.

[22]  J. Schmutz,et al.  Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? , 2015, Scientific Reports.

[23]  J. Qi,et al.  Saccharina genomes provide novel insight into kelp biology , 2015, Nature Communications.

[24]  L. Vasseur,et al.  Characterization and expression of the cytochrome P450 gene family in diamondback moth, Plutella xylostella (L.) , 2015, Scientific Reports.

[25]  T. Mock,et al.  Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage , 2015, The Plant journal : for cell and molecular biology.

[26]  Bo Hu,et al.  GSDS 2.0: an upgraded gene feature visualization server , 2014, Bioinform..

[27]  G. Johnsen,et al.  System Responses to Equal Doses of Photosynthetically Usable Radiation of Blue, Green, and Red Light in the Marine Diatom Phaeodactylum tricornutum , 2014, PloS one.

[28]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[29]  B. Hamberger,et al.  Cytochrome P450-mediated metabolic engineering: current progress and future challenges. , 2014, Current opinion in plant biology.

[30]  Sarah R. Smith,et al.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing , 2014, PLoS biology.

[31]  Inna Dubchak,et al.  The genome portal of the Department of Energy Joint Genome Institute: 2014 updates , 2013, Nucleic Acids Res..

[32]  T. Tonon,et al.  Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae , 2014, BMC Plant Biology.

[33]  R. Riley,et al.  Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora , 2013, Mycologia.

[34]  A. Osbourn,et al.  Biochemical analysis of a multifunctional cytochrome P450 (CYP51) enzyme required for synthesis of antimicrobial triterpenes in plants , 2013, Proceedings of the National Academy of Sciences.

[35]  P. Keeling,et al.  The number, speed, and impact of plastid endosymbioses in eukaryotic evolution. , 2013, Annual review of plant biology.

[36]  F. Guengerich,et al.  Unusual Cytochrome P450 Enzymes and Reactions* , 2013, The Journal of Biological Chemistry.

[37]  D. Nelson,et al.  The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[38]  I. Phillips,et al.  Cytochrome P450 Protocols , 1998, Methods in Molecular Biology.

[39]  Haoli Ma,et al.  Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.) , 2012, PloS one.

[40]  Inna Dubchak,et al.  The Genome Portal of the Department of Energy Joint Genome Institute , 2011, Nucleic Acids Res..

[41]  Corinne Da Silva,et al.  The Ectocarpus genome and brown algal genomics: the Ectocarpus Genome Consortium , 2012 .

[42]  R. Carvalho,et al.  Transcriptomics Responses in Marine Diatom Thalassiosira pseudonana Exposed to the Polycyclic Aromatic Hydrocarbon Benzo[a]pyrene , 2011, PloS one.

[43]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[44]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[45]  Igor B. Rogozin,et al.  A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes , 2011, PLoS Comput. Biol..

[46]  T. Brembu,et al.  Genome-wide profiling of responses to cadmium in the diatom Phaeodactylum tricornutum. , 2011, Environmental science & technology.

[47]  Corinne Da Silva,et al.  The Ectocarpus genome and the independent evolution of multicellularity in brown algae , 2010, Nature.

[48]  Daisaku Ohta,et al.  Diversification of P450 genes during land plant evolution. , 2010, Annual review of plant biology.

[49]  Kuo-Chen Chou,et al.  A New Method for Predicting the Subcellular Localization of Eukaryotic Proteins with Both Single and Multiple Sites: Euk-mPLoc 2.0 , 2010, PloS one.

[50]  M. Csűrös,et al.  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. , 2010, Bioinformatics.

[51]  Kasper Hancke,et al.  An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum , 2009, PloS one.

[52]  P. Lopez,et al.  Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters , 2009, PloS one.

[53]  D. Nelson The Cytochrome P450 Homepage , 2009, Human Genomics.

[54]  Debashish Bhattacharya,et al.  Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms , 2009, Science.

[55]  I. Feussner,et al.  Biosynthesis of oxylipins in non-mammals. , 2009, Progress in lipid research.

[56]  D. Kelly,et al.  The CYPome (Cytochrome P450 complement) of Aspergillus nidulans. , 2009, Fungal genetics and biology : FG & B.

[57]  P. Rouzé,et al.  Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress , 2009, Genome Biology.

[58]  A. Grossman,et al.  Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. , 2008, Molecular biology and evolution.

[59]  T. Tonon,et al.  Copper stress induces biosynthesis of octadecanoid and eicosanoid oxygenated derivatives in the brown algal kelp Laminaria digitata , 2008 .

[60]  Thomas Mock,et al.  Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses , 2008, Proceedings of the National Academy of Sciences.

[61]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[62]  D. Penny,et al.  A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. , 2007, Molecular biology and evolution.

[63]  M. Waterman,et al.  Sterol 14α-Demethylase Cytochrome P450 (CYP51), a P450 in all Biological Kingdoms , 2007 .

[64]  G. Pohnert,et al.  Biosynthesis of polyunsaturated short chain aldehydes in the diatom Thalassiosira rotula. , 2007, Organic letters.

[65]  R. Dean,et al.  The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes , 2007, BMC Evolutionary Biology.

[66]  A. Osbourn,et al.  A different function for a member of an ancient and highly conserved cytochrome P450 family: From essential sterols to plant defense , 2006, Proceedings of the National Academy of Sciences.

[67]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[68]  A. Fontana,et al.  Biosynthetic intermediates and stereochemical aspects of aldehyde biosynthesis in the marine diatom Thalassiosira rotula. , 2006, Phytochemistry.

[69]  J. Stegeman,et al.  A Revised Evolutionary History of the CYP1A Subfamily: Gene Duplication, Gene Conversion, and Positive Selection , 2006, Journal of Molecular Evolution.

[70]  Ho Bang Kim,et al.  Arabidopsis cyp51 Mutant Shows Postembryonic Seedling Lethality Associated with Lack of Membrane Integrity1[w] , 2005, Plant Physiology.

[71]  Jonathan Pevsner,et al.  Basic Local Alignment Search Tool (BLAST) , 2005 .

[72]  Søren Bak,et al.  Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot1[w] , 2004, Plant Physiology.

[73]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[74]  L. Tian,et al.  The Arabidopsis LUT1 locus encodes a member of the cytochrome P450 family that is required for carotenoid ε-ring hydroxylation activity , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Yuuki Takada,et al.  Novel oxylipin metabolites from the brown alga Eisenia bicyclis. , 2003, Journal of natural products.

[76]  K. Matsui,et al.  Hydroperoxy-arachidonic acid mediated n-hexanal and (Z)-3- and (E)-2-nonenal formation in Laminaria angustata. , 2003, Phytochemistry.

[77]  R. Kong,et al.  IDENTIFICATION OF A NOVEL CYTOCHROME P450 cDNA, CYP97E1, FROM THE MARINE DIATOM SKELETONEMA COSTATUM BACILLARIOPHYCEAE 1 , 2003 .

[78]  T. Kajiwara,et al.  C6-Aldehyde Formation by Fatty Acid Hydroperoxide Lyase in the Brown Alga Laminaria angustata , 2003, Zeitschrift fur Naturforschung. C, Journal of biosciences.

[79]  R. Voorrips MapChart: software for the graphical presentation of linkage maps and QTLs. , 2002, The Journal of heredity.

[80]  S. Horvat,et al.  Characterization of the mouse lanosterol 14alpha-demethylase (CYP51), a new member of the evolutionarily most conserved cytochrome P450 family. , 2000, Archives of biochemistry and biophysics.

[81]  S. Pflugmacher,et al.  Cytochrome P450 monooxygenases for fatty acids and xenobiotics in marine macroalgae. , 1998, Plant physiology.

[82]  D. Nelson,et al.  Cytochrome P450 nomenclature. , 1998, Methods in molecular biology.

[83]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[84]  Benveniste,et al.  Cytochrome P450 , 1993, Handbook of Experimental Pharmacology.

[85]  W. Gerwick,et al.  Cymathere ethers A and B : bicyclic oxylipins from the marine brown alga Cymathere triplicata , 1992 .

[86]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[87]  J. Farris Phylogenetic Analysis Under Dollo's Law , 1977 .