An improved and general streamlined phylogenetic protocol applied to the fatty acid desaturase family
Tài liệu tham khảo
Ahola, 2006, A statistical score for assessing the quality of multiple sequence alignments, BMC Bioinf., 7, 484, 10.1186/1471-2105-7-484
Altabe, 2003, The Bacillus subtilis acyl lipid desaturase is a Δ5 desaturase, J. Bacteriol., 185, 3228, 10.1128/JB.185.10.3228-3231.2003
Apiradee, 2004, The expression of three desaturase genes of Spirulina platensis in Escherichia coli DH5α – heterologous expression of Spirulina-desaturase genes, Mol. Biol. Rep., 31, 177, 10.1023/B:MOLE.0000043571.78809.40
Bai, 2015, X-ray structure of a mammalian stearoyl-CoA desaturase, Nature, 524, 252, 10.1038/nature14549
Blackburne, 2012, Measuring the distance between multiple sequence alignments, Bioinformatics, 28, 495, 10.1093/bioinformatics/btr701
Busk, 2013, Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs, Appl. Environ. Microbiol., 79, 3380, 10.1128/AEM.03803-12
Busk, 2015, Classification of fungal and bacterial lytic polysaccharide monooxygenases, BMC Genomics, 16, 368, 10.1186/s12864-015-1601-6
Busk, 2014, Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature, PLoS ONE, 9, e114138, 10.1371/journal.pone.0114138
Castresana, 2000, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol. Biol. Evol., 17, 540, 10.1093/oxfordjournals.molbev.a026334
Chang, 2006, Identification of Rv3230c as the NADPH oxidoreductase of a two-protein DesA3 acyl-CoA desaturase in Mycobacterium tuberculosis H37Rv, Biochemistry, 45, 13476, 10.1021/bi0615285
Cheevadhanarak, 2012, Draft genome sequence of Arthrospira platensis C1 (PCC9438), Standards Genomic Sci., 6, 43, 10.4056/sigs.2525955
Deshnium, 2000, Temperature-independent and -dependent expression of desaturase genes in filamentous cyanobacterium Spirulina platensis strain C1 (Arthrospira sp. PCC 9438), FEMS Microbiol. Lett., 184, 207, 10.1111/j.1574-6968.2000.tb09015.x
Dessimoz, 2010, Phylogenetic assessment of alignments reveals neglected tree signal in gaps, Genome Biol., 11, R37, 10.1186/gb-2010-11-4-r37
Dwivedi, 2009, Phylogenetic inference under varying proportions of indel-induced alignment gaps, BMC Evol. Biol., 9, 211, 10.1186/1471-2148-9-211
Edgar, 2006, Multiple sequence alignment, Curr. Opin. Struct. Biol., 16, 368, 10.1016/j.sbi.2006.04.004
Golubchik, 2007, Mind the gaps: evidence of bias in estimates of multiple sequence alignments, Mol. Biol. Evol., 24, 2433, 10.1093/molbev/msm176
Gouy, 2010, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 27, 221, 10.1093/molbev/msp259
Hall, 2013, Building phylogenetic trees from molecular data with MEGA, Mol. Biol. Evol., 30, 1229, 10.1093/molbev/mst012
Heilmann, 2004, Switching desaturase enzyme specificity by alternate subcellular targeting, Proc. Natl. Acad. Sci. USA, 101, 10266, 10.1073/pnas.0402200101
Holmes, 2003, Bootstrapping phylogenetic trees: theory and methods, Stat. Sci., 18, 241, 10.1214/ss/1063994979
Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010
Katoh, 2008, Recent developments in the MAFFT multiple sequence alignment program, Brief. Bioinform., 9, 286, 10.1093/bib/bbn013
Letsch, 2010, The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods, Mol. Biol. Evol., 27, 2507, 10.1093/molbev/msq140
Li, 2016, Classification and substrate head-group specificity of membrane fatty acid desaturases, Comput. Struct. Biotechnol. J., 14, 341, 10.1016/j.csbj.2016.08.003
López Alonso, 2003, Evolution of the membrane-bound fatty acid desaturases, Biochem. Syst. Ecol., 31, 1111, 10.1016/S0305-1978(03)00041-3
Löytynoja, 2008, Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis, Science, 320, 1632, 10.1126/science.1158395
Michaelson, 2013, Identification of a cytochrome b5-fusion desaturase responsible for the synthesis of triunsaturated sphingolipid long chain bases in the marine diatom Thalassiosira pseudonana, Phytochemistry, 90, 50, 10.1016/j.phytochem.2013.02.010
Minh, 2013, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol., 30, 1188, 10.1093/molbev/mst024
Misof, 2014, Phylogenomics resolves the timing and pattern of insect evolution, Science, 346, 763, 10.1126/science.1257570
Mount, D.W., 2008. Choosing a Method for Phylogenetic Prediction. Cold Spring Harbor Protocols. pdb.ip49.
Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300
Nuin, 2006, The accuracy of several multiple sequence alignment programs for proteins, BMC Bioinf., 7, 471, 10.1186/1471-2105-7-471
Peyou-Ndi, 2000, Identification and characterization of an animal Δ12 Fatty Acid desaturase gene by heterologous expression in Saccharomyces cerevisiae, Arch. Biochem. Biophys., 376, 399, 10.1006/abbi.2000.1733
Serra, 2007, A multifunctional desaturase involved in the biosynthesis of the processionary moth sex pheromone, Proc. Natl. Acad. Sci., 104, 16444, 10.1073/pnas.0705385104
Sperling, 2003, The evolution of desaturases, Prostaglandins Leukot. Essent. Fatty Acids, 68, 73, 10.1016/S0952-3278(02)00258-2
Ternes, 2002, Identification and characterization of a sphingolipid Δ4-desaturase family, J. Biol. Chem., 277, 25512, 10.1074/jbc.M202947200
Warnow, T., 2012. Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. PLoS Currents, 4, RRN1308.
Whelan, 2007, New approaches to phylogenetic tree search and their application to large numbers of protein alignments, Syst. Biol., 56, 727, 10.1080/10635150701611134
Zhou, 2007, Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis, Phytochemistry, 68, 785, 10.1016/j.phytochem.2006.12.016
Zhou, 2008, Isolation and functional characterization of two independently-evolved fatty acid Δ12-desaturase genes from insects, Insect Mol. Biol., 17, 667, 10.1111/j.1365-2583.2008.00841.x
Zhu, 2015, The crystal structure of an integral membrane fatty acid α-hydroxylase, J. Biol. Chem., 290, 29820, 10.1074/jbc.M115.680124