title: Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).
abstract: Citrus are among the economically most important fruit tree crops in the world. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa infection, is a serious disease limiting citrus production at a global scale. With availability of citrus genomic resources, it is now possible to compare citrus expressed sequence tag (EST) data sets and identify single-nucleotide polymorphisms (SNPs) within and among different citrus cultivars that can be exploited for citrus resistance to infections, citrus breeding, among others. We report here, for the first time, SNPs in the EST data sets of X. fastidiosa-infected Citrus sinensis (sweet orange) and their functional annotation that revealed the involvement of eight C. sinensis candidate genes in CVC pathogenesis. Among these genes were xyloglucan endotransglycosylase, myo-inositol-1-phosphate synthase, and peroxidase were found to be involved in plant cell wall metabolism. These have been further investigated by molecular modeling for their role in CVC infection and defense. Molecular docking analyses of the wild and the mutant (SNP containing) types of the selected three enzymes with their respective substrates revealed a significant decrease in the binding affinity of substrates for the mutant enzymes, thus suggesting a decrease in the catalytic efficiency of these enzymes during infection, thereby facilitating a favorable condition for infection by the pathogen. These findings offer novel agrigenomics insights in developing future molecular targets and strategies for citrus fruit cultivation in ways that are resistant to X. fastidiosa infection, and by extension, with greater harvesting efficiency and economic value.
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Upendra N
authors.initials: UN
authors.lastname: Dwivedi
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Sameeksha
authors.initials: S
authors.lastname: Tiwari
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Pragya
authors.initials: P
authors.lastname: Prasanna
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Manika
authors.initials: M
authors.lastname: Awasthi
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Swati
authors.initials: S
authors.lastname: Singh
authors.affiliation: Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .
authors.forename: Veda P
authors.initials: VP
authors.lastname: Pandey
mesh_terms: D032084:Citrus sinensis / Q000235:genetics* / Q000382:microbiology; D018556:Crops, Agricultural; D023281:Genomics; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide; D044167:Xylella / Q000472:pathogenicity*