Genome-wide identification and functional analysis of the horizontally transferred genes in Penicillium
Tài liệu tham khảo
Abraham, 1940, An enzyme from bacteria able to destroy penicillin, Nature, 146, 837, 10.1038/146837a0
Aminov, 2010, A brief history of the antibiotic era: lessons learned and challenges for the future, Front. Microbiol., 1, 134, 10.3389/fmicb.2010.00134
Armenteros, 2019, SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat. Biotechnol., 37, 420, 10.1038/s41587-019-0036-z
Ballester, 2015, Genome, transcriptome, and functional analyses of Penicillium expansum provide new insights into secondary metabolism and pathogenicity, Mol. Plant-Microbe Interact., 28, 232, 10.1094/MPMI-09-14-0261-FI
Banani, 2016, Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum, BMC Genomics, 17, 19, 10.1186/s12864-015-2347-x
van den Berg, 2008, Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum, Nat. Biotechnol., 26, 1161, 10.1038/nbt.1498
Capella-Gutierrez, 2009, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, 25, 1972, 10.1093/bioinformatics/btp348
Cheeseman, 2014, Multiple recent horizontal transfers of a large genomic region in cheese making fungi, Nat. Commun., 5, 1, 10.1038/ncomms3876
Conesa AGotz, 2008, Blast2GO: A comprehensive suite for functional analysis in plant genomics, Int J Plant Genomics, 619832, 619832
Emanuelsson, 2000, Predicting subcellular localization of proteins based on their N-terminal amino acid sequence, J. Mol. Biol., 300, 1005, 10.1006/jmbi.2000.3903
Fankhauser NMäser, 2005, Identification of GPI anchor attachment signals by a Kohonen self-organizing map, Bioinformatics, 21, 1846, 10.1093/bioinformatics/bti299
Finn, 2014, Pfam: the protein families database, Nucleic Acids Res., 42, 27, 10.1093/nar/gkt1223
Fitzpatrick, 2012, Horizontal gene transfer in fungi, FEMS Microbiol. Lett., 329, 1, 10.1111/j.1574-6968.2011.02465.x
Friesen, 2006, Emergence of a new disease as a result of interspecific virulence gene transfer, Nat. Genet., 38, 953, 10.1038/ng1839
Fu, 2012, CD-HIT: accelerated for clustering the next-generation sequencing data, Bioinformatics, 28, 3150, 10.1093/bioinformatics/bts565
Gao, 2019, Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism, Fungal Genet. Biol., 128, 60, 10.1016/j.fgb.2019.04.002
Gilbert CCordaux, 2013, Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes, Genome Biol. Evol., 5, 822, 10.1093/gbe/evt057
Gonçalves, 2018, Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage, eLife, 7, 10.7554/eLife.33034
Grijseels, 2016, Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites, Sci. Rep., 6, 35112, 10.1038/srep35112
Horn, 2015, Draft genome sequence of the fungus Penicillium brasilianum MG11, Genome Announc, 3, 10.1128/genomeA.00724-15
Husnik FMcCutcheon JP., 2018, Functional horizontal gene transfer from bacteria to eukaryotes, Nat. Rev. Microbiol., 16, 67, 10.1038/nrmicro.2017.137
Jaramillo, 2015, Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer, BMC Genomics, 16, 2, 10.1186/1471-2164-16-2
Keeling PJPalmer JD., 2008, Horizontal gene transfer in eukaryotic evolution, Nat. Rev. Genet., 9, 605, 10.1038/nrg2386
Kim, 2019, Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat. Biotechnol., 37, 907, 10.1038/s41587-019-0201-4
Kominek, 2019, Eukaryotic acquisition of a bacterial operon, Cell, 176, 1356, 10.1016/j.cell.2019.01.034
Kurland, 2003, Horizontal gene transfer: a critical view, Proc. Natl. Acad. Sci., 100, 9658, 10.1073/pnas.1632870100
Letunic IBork, 2019, Interactive tree of life (iTOL) v4: recent updates and new developments, Nucleic Acids Res., 47, W256, 10.1093/nar/gkz239
Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656
Lieber, 2010, The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway, Annu. Rev. Biochem., 79, 181, 10.1146/annurev.biochem.052308.093131
Liu, 2013, Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens, PLoS One, 8
Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8
Marcet-Houben MGabaldón, 2010, Acquisition of prokaryotic genes by fungal genomes, Trends Genet., 26, 5, 10.1016/j.tig.2009.11.007
Marcet-Houben, 2012, Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus, BMC Genomics, 13, 646, 10.1186/1471-2164-13-646
Mehrabi, 2011, Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range, FEMS Microbiol. Rev., 35, 542, 10.1111/j.1574-6976.2010.00263.x
Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300
Nielsen, 2017, Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species, Nat. Microbiol., 2, 1, 10.1038/nmicrobiol.2017.44
Nielsen, 2019, Comparative transcriptome analysis shows conserved metabolic regulation during production of secondary metabolites in filamentous Fungi, Msystems, 4, e00012, 10.1128/mSystems.00012-19
Qiu, 2016, Extensive horizontal gene transfers between plant pathogenic fungi, BMC Biol., 14, 41, 10.1186/s12915-016-0264-3
Reynolds, 2016, Phylogenomic analysis supports a recent change in nitrate assimilation in the white-nose syndrome pathogen, Pseudogymnoascus destructans, Fungal Ecol., 23, 20, 10.1016/j.funeco.2016.04.010
Richards TATalbot NJ., 2013, Horizontal gene transfer in osmotrophs: playing with public goods, Nat. Rev. Microbiol., 11, 720, 10.1038/nrmicro3108
Richardson, 2018, Gene exchange drives the ecological success of a multi-host bacterial pathogen, Nat. Ecol. Evol., 2, 1468, 10.1038/s41559-018-0617-0
Ruan, 2017, Functional analysis of two sterol regulatory element binding proteins in Penicillium digitatum, PLoS One, 12, 10.1371/journal.pone.0176485
Ruan, 2019, Functional diversification of sterol regulatory element binding proteins following gene duplication in a fungal species, Fungal Genet. Biol., 131, 103239, 10.1016/j.fgb.2019.103239
Saier, 2016, The transporter classification database (TCDB): recent advances, Nucleic Acids Res., 44, 5, 10.1093/nar/gkv1103
Shen, 2018, Tempo and mode of genome evolution in the budding yeast subphylum, Cell, 175, 1533, 10.1016/j.cell.2018.10.023
Soanes DRichards, 2014, Horizontal gene transfer in eukaryotic plant pathogens, Annu. Rev. Phytopathol., 52, 583, 10.1146/annurev-phyto-102313-050127
Soucy, 2015, Horizontal gene transfer: building the web of life, Nat. Rev. Genet., 16, 472, 10.1038/nrg3962
Steenwyk JLRokas, 2019, Treehouse: a user-friendly application to obtain subtrees from large phylogenies, BMC research notes, 12, 1
Steenwyk, 2019, A robust phylogenomic time tree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium, mBio, 10, 10.1128/mBio.00925-19
Stevenson, 2017, Gene mobility promotes the spread of resistance in bacterial populations, ISME J., 11, 1930, 10.1038/ismej.2017.42
Visagie, 2014, Identification and nomenclature of the genus Penicillium, Stud. Mycol., 78, 343, 10.1016/j.simyco.2014.09.001
Wang, 2015, PdbrlA, PdabaA and PdwetA control distinct stages of conidiogenesis in Penicillium digitatum, Res. Microbiol., 166, 56, 10.1016/j.resmic.2014.12.003
Wang, 2019, A small horizontally transferred gene cluster contributes to the sporulation of Alternaria alternata, Genome Biol. Evol., 11, 3436, 10.1093/gbe/evz257
Wisecaver, 2016, Dynamic evolution of nitric oxide detoxifying Flavohemoglobins, a family of single-protein metabolic modules in Bacteria and eukaryotes, Mol. Biol. Evol., 33, 1979, 10.1093/molbev/msw073
Yamada, 2016, Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees, Bioinformatics, 32, 3246, 10.1093/bioinformatics/btw412
Zhang, 2018, dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Res., 46, W95, 10.1093/nar/gky418