title: Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome.
abstract: Citrus blight is a citrus tree overall decline disease and causes serious losses in the citrus industry worldwide. Although it was described more than one hundred years ago, its causal agent remains unknown and its pathophysiology is not well determined, which hampers our understanding of the disease and design of suitable disease management.
  
  
  
  In this study, we sequenced and assembled the draft genome for Swingle citrumelo, one important citrus rootstock. The draft genome is approximately 280 Mb, which covers 74 % of the estimated Swingle citrumelo genome and the average coverage is around 15X. The draft genome of Swingle citrumelo enabled us to conduct transcriptome analysis of roots of blight and healthy Swingle citrumelo using RNA-seq. The RNA-seq was reliable as evidenced by the high consistence of RNA-seq analysis and quantitative reverse transcription PCR results (R(2) = 0.966). Comparison of the gene expression profiles between blight and healthy root samples revealed the molecular mechanism underneath the characteristic blight phenotypes including decline, starch accumulation, and drought stress. The JA and ET biosynthesis and signaling pathways showed decreased transcript abundance, whereas SA-mediated defense-related genes showed increased transcript abundance in blight trees, suggesting unclassified biotrophic pathogen was involved in this disease.
  
  
  
  Overall, the Swingle citrumelo draft genome generated in this study will advance our understanding of plant biology and contribute to the citrus breeding. Transcriptome analysis of blight and healthy trees deepened our understanding of the pathophysiology of citrus blight.
authors.affiliation: Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA.
authors.forename: Yunzeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Barthe
authors.affiliation: Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL, USA.
authors.forename: Jude W
authors.initials: JW
authors.lastname: Grosser
authors.affiliation: Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA. nianwang@ufl.edu.
authors.forename: Nian
authors.initials: N
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods; D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D063990:Gene Ontology; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
keywords: Citrus blight; Genome assembly; RNA-seq; Root; Swingle citrumelo