New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange (Citrus sinensis)

References

• Jacques MA, Arlat M, Boulanger A, et al. Using ecology, physiology, and genomics to understand host specificity in Xanthomonas. Annu Rev Phytopathol. 2016;54(163–187).
   PubMedGoogle Scholar
• Stukenbrock EH. Evolution, selection and isolation: A genomic view of speciation in fungal plant pathogens. New Phytol. 2013;199(4):895–907.
   PubMed Web of Science ®Google Scholar
• Friesen TL, Stukenbrock EH, Liu Z, et al. Emergence of a new disease as a result of interspecific virulence gene transfer. Nat Genet. 2006;38(8):953–956.
   PubMed Web of Science ®Google Scholar
• Giraud T, Gladieux P, Gavrilets S. Linking the emergence of fungal plant diseases with ecological speciation. Trends Ecol Evol. 2010;25(7):387–395.
   PubMed Web of Science ®Google Scholar
• Vilanova L, Vinas I, Torres R, et al. Infection capacities in the orange-pathogen relationship: Compatible (Penicillium digitatum) and incompatible (Penicillium expansum) interactions. Food Microbiol. 2012;29(1):56–66.
   PubMed Web of Science ®Google Scholar
• Marcet-Houben M, Ballester AR, de la Fuente B, et al. Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics. 2012;13:646.
   PubMed Web of Science ®Google Scholar
• Ballester A-R, Marcet-Houben M, Levin E, et al. Genome, transcriptome, and functional analyses of Penicillium expansum provide new insights Into secondary metabolism and pathogenicity. Mol Plant Microbe Interact. 2015;28(3):232–248.
   PubMed Web of Science ®Google Scholar
• Li B, Zong Y, Du Z, et al. Genomic characterization reveals insights into patulin biosynthesis and pathogenicity in Penicillium species. Mol Plant Microbe Interact. 2015;28(6):635–647.
   PubMed Web of Science ®Google Scholar
• Julca I, Droby S, Sela N, et al. Contrasting genomic diversity in two cosely related postharvest pathogens: Penicillium digitatum and Penicillium expansum. Genome Biol Evol. 2016;8(1):218–227.
   Web of Science ®Google Scholar
• Marcet-Houben M, Gabaldon T. Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi. Fungal Genet Biol. 2016;86:71–80.
   PubMed Web of Science ®Google Scholar
• Marchler-Bauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 2015;43(D1):D222–D226.
   PubMed Web of Science ®Google Scholar
• Ma M, Wang Z, Li L, et al. Complete genome sequence of Paenibacillus mucilaginosus 3016, a bacterium functional as microbial fertilizer. J Bacteriol. 2012;194(10):2777–2778.
   PubMed Web of Science ®Google Scholar
• Niehaus EM, Muensterkoetter M, Proctor RH, et al. Comparative “omics” of the fusarium fujikuroi species complex highlights differences in genetic potential and metabolite synthesis. Genome Biol Evol. 2016;8(11):3574–3599.
   PubMed Web of Science ®Google Scholar
• Sanchez-Vallet A, Fouche S, Fudal I, et al. The genome biology of effector gene evolution in filamentous plant pathogens. Annu Rev Phytopathol. 2018;56(1):21–40.
   PubMedGoogle Scholar
• Lu S, Edwards MC. Genome-wide analysis of small secreted cysteine-rich proteins identifies candidate effector proteins potentially involved in Fusarium graminearum-wheat interactions. Phytopathology. 2016;106(2):166–176.
   PubMed Web of Science ®Google Scholar
• Garrigues S, Gandia M, Castillo L, et al. Three antifungal proteins from Penicillium expansum: Different patterns of production and antifungal activity. Front Microbiol. 2018;9:2370.
   PubMed Web of Science ®Google Scholar
• Looi HK, Toh YF, Yew SM, et al. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola. Peer J. 2017;5:e2841.
   PubMed Web of Science ®Google Scholar
• Satjarak A, Graham LE, Verbruggen H. Genome-wide analysis of carbohydrate-active enzymes Pyramimonas parkeae (Prasinophyceae). J Phycol. 2017;53(5):1072–1086.
   PubMed Web of Science ®Google Scholar
• Bautista-Banos S. Postharvest Decay Control Strategies. Chapter 2 Penicillium digitatum, Penicillium italicum (Green Mold, Blue Mold); Elsevier, Academic Press; 2014, p.45–102.
   Google Scholar
• Banani H, Marcet-Houben M, Ballester AR, et al. Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. BMC Genomics. 2016;17(1):19.
   PubMedGoogle Scholar
• Yoshida K, Saunders DGO, Mitsuoka C, et al. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics. 2016;17(1):370.
   PubMedGoogle Scholar
• Shen Q, Liu Y, Naqvi NI. Fungal effectors at the crossroads of phytohomone singaling. Curr Opin Microbiol. 2018;46:1–6.
   PubMed Web of Science ®Google Scholar
• Lopez D, Ribeiro S, Label P, et al. Genome-wide analysis of Corynespora cassiicola leaf fall disease putative effectors. Front Microbiol. 2018;9:276.
   PubMed Web of Science ®Google Scholar
• Moreira LRS, Filho EXF. An overview of mannan structure and mannan-degrading enzyme systems. Appl Microbiol Biotechnol. 2008;79(2):165–178.
   PubMed Web of Science ®Google Scholar
• Del Carmen Rodriguez-Gacio M, Iglesias-Fernandez R, Carbonero P, et al. Softening-up mannan-rich cell walls. J Exp Bot. 2012;63(11):3975–3988.
   Web of Science ®Google Scholar
• Baath JA, Giummarella N, Klaubauf S, et al. A glucuronoyl esterase from Acremonium alcalophilum cleaves native lignin-carbohydrate ester bonds. FEBS Lett. 2016;590(16):2611–2618.
   PubMed Web of Science ®Google Scholar
• Kumamoto CA. Molecular mechanisms of mechanosensing and their roles in fungal contact sensing. Nat Rev Microbiol. 2008;6(9):667–673.
   PubMed Web of Science ®Google Scholar
• Que Y, Xu L, Wu Q, et al. Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut. BMC Genomics. 2014;15(1):996.
   PubMedGoogle Scholar
• Dean RA, Talbot NJ, Ebbole DJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 2005;434(7036):980–986.
   PubMed Web of Science ®Google Scholar
• Goldstone JV, Goldstone HMH, Morrison AM, et al. Cytochrome p450 1 genes in early deuterostomes (tunicates and sea urchins) and vertebrates (chicken and frog): Origin and diversification of the CYP1 gene family. Mol Biol Evol. 2007;24(12):2619–2631.
   PubMed Web of Science ®Google Scholar
• Fox EM, Howlett BJ. Secondary metabolism: regulation and role in fungal biology.Curr Opin Microbiol. [2008]; 11(6):481–487.
   PubMed Web of Science ®Google Scholar
• Hu X, Xiao G, Zheng P, et al. Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation. Proc Natl Acad Sci U S A. 2014;111(47):16796–16801.
   PubMed Web of Science ®Google Scholar
• Ma LJ, van der Does HC, Borkovich KA, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010;464(7287):367–373.
   PubMed Web of Science ®Google Scholar
• Wang S, Leclerque A, Pava-Ripoll M, et al. Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae. Eukaryot Cell. 2009;8(6):888–898.
   PubMedGoogle Scholar
• Sharma R, Mishra B, Runge F, et al. Gene loss rather than gene gain Is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum. Genome Biol Evol. 2014;6(8):2034–2049.
   PubMed Web of Science ®Google Scholar
• Elbarbary RA, Lucas BA, Maquat LE. Retrotransposons as regulators of gene expression. Science. 2016;351(6274).
   PubMed Web of Science ®Google Scholar
• Zhang L, Huang X, He C, et al. Novel fungal pathogenicity and leaf defense strategies are revealed by simultaneous transcriptome analysis of Colletotrichum fructicola and strawberry infected by this fungus. Front Plant Sci. 2018;9:434.
   PubMed Web of Science ®Google Scholar
• Li P, Liu W, Zhang Y, et al. Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems. Sci Rep. 2019;9(1):10111.
   PubMedGoogle Scholar
• Wu G, Ii WM J, Lichtner FJ, et al. Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay. Peer J. 2019;7:e6170.
   PubMed Web of Science ®Google Scholar
• Houterman PM, Cornelissen BJC, Rep M. Suppression of plant resistance gene-based immunity by a fungal effector. PLoS Pathog. 2008;4(5):e1000061.
   PubMed Web of Science ®Google Scholar
• El Hadrami A, El-Bebany AF, Yao Z, et al. Plants versus fungi and oomycetes: pathogenesis, defense and counter-defense in the proteomics era. Int J Mol Sci. 2012;13(6):7237–7259.
   PubMed Web of Science ®Google Scholar
• Bradshaw RE, Guo Y, Sim AD, et al. Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata. Mol Plant Pathol. 2016;17(2):210–224.
   PubMed Web of Science ®Google Scholar
• Alkan N, Friedlander G, Ment D, et al. Simultaneous transcriptome analysis of Colletotrichum gloeosporioides and tomato fruit pathosystem reveals novel fungal pathogenicity and fruit defense strategies. New Phytol. 2015;205(2):801–815.
   PubMed Web of Science ®Google Scholar
• Zheng F, Wu H, Zhang R, et al. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics. 2016;17(1):402.
   PubMedGoogle Scholar
• Tayeh C, Randoux B, Vincent D, et al. Exogenous trehalose induces defenses in wheat before and during a biotic stress caused by powdery mildew. Phytopathology. 2014;104(3):293–305.
   PubMed Web of Science ®Google Scholar
• Zhang H, Hong Y, Huang L, et al. Virus-induced gene silencing-based functional analyses revealed the involvement of several putative trehalose-6-phosphate synthase/phosphatase genes in disease resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in tomato. Front Plant Sci. 2016;7:1176.
   PubMed Web of Science ®Google Scholar
• Wingler A. The function of trehalose biosynthesis in plants. Phytochemistry. 2002;60(5):437–440.
   PubMed Web of Science ®Google Scholar
• Sanchez-Rangel D, Rivas-San Vicente M, Eugenia de la Torre-hernandez M, et al. Deciphering the link between salicylic acid signaling and sphingolipid metabolism. Front Plant Sci. 2015;6:125.
   PubMed Web of Science ®Google Scholar
• La Mantia J, Unda F, Douglas CJ, et al. Overexpression of AtGolS3 and CsRFS in poplar enhances ROS tolerance and represses defense response to leaf rust disease. Tree Physiol. 2018;38(3):457–470.
   PubMed Web of Science ®Google Scholar
• Aksic MMF, Dabic DC, Gasic UM, et al. Polyphenolic profile of pear leaves with different resistance to pear psylla (Cacopsylla pyri). J Agric Food Chem. 2015;63(34):7476–7486.
   PubMed Web of Science ®Google Scholar
• Birney E, Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 2000;10(4):547–548.
   PubMed Web of Science ®Google Scholar
• Stanke M, Keller O, Gunduz I, et al. AUGUSTUS: Ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34(Web Server):W435–W439.
   PubMedGoogle Scholar
• Khaldi N, Seifuddin FT, Turner G, et al. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 2010;47(9):736–741.
   PubMed Web of Science ®Google Scholar
• Kall L, Krogh A, Sonnhammer ELL. A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004;338(5):1027–1036.
   PubMed Web of Science ®Google Scholar
• Ernst J, Bar-Joseph Z. STEM: A tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006;7(1):191.
   PubMedGoogle Scholar
• Ruan J, Li H, Chen Z, et al. TreeFam: 2008 update. Nucleic Acids Res. 2008;36(Database):D735–D740.
   PubMedGoogle Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
   PubMed Web of Science ®Google Scholar
• Cui Y, Yu C, Yan Y, et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A. 2013;110(2):577–582.
   PubMed Web of Science ®Google Scholar
• Yang ZH, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000;17(1):32–43.
   PubMed Web of Science ®Google Scholar
• Nikoh N, McCutcheon JP, Kudo T, et al. Bacterial genes in the aphid genome: Absence of functional gene transfer from Buchnera to its host. PLoS Genet. 2010;6(2):e1000827.
   PubMed Web of Science ®Google Scholar
• Li R, Yu C, Li Y, et al. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966–1967.
   PubMed Web of Science ®Google Scholar
• Li B, Dewey CN. RSEM: Accurate transcript quantific4ation from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12(1):323.
   PubMed Web of Science ®Google Scholar
• Tarazona S, Furio-Tari P, Turra D, et al. Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res. 2015;43(21):e140.
   PubMed Web of Science ®Google Scholar
• Jiang G, Xiao L, Yan H, et al. Redox regulation of methionine in calmodulin affects the activity levels of senescence-related transcription factors in litchi. Biochim Biophys Acta Gen Subj. 2017;1861(5):1140–1151.
   PubMed Web of Science ®Google Scholar
• Dunn WB, Broadhurst D, Begley P, et al. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc. 2011;6(7):1060–1083.
   PubMed Web of Science ®Google Scholar
• Chen D, Lin S, Xu W, et al. Qualitative and quantitative analysis of the major constituents in shexiang tongxin dropping Pill by HPLC-Q-TOF-MS/MS and UPLC-QqQ-MS/MS. Molecules. 2015;20(10):18597–18619.
   PubMed Web of Science ®Google Scholar
• Hsu HH, Araki M, Mochizuki M, et al. A systematic approach to timeseries metabolite profiling and RNA-seq analysis of Chinese hamster ovary cell culture. Sci Rep. 2017;7:43518.
   PubMed Web of Science ®Google Scholar