title: De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes.
abstract: Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium×hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance toPythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome. De novo assembly of the reads resulted in approximately 130,000 unigenes. Based on bioinformatic analysis, 71,825 (52.3%) caladium unigenes were annotated for putative functions, 48,417 (67.4%) and 31,417 (72.7%) were assigned to Gene Ontology (GO) and Clusters of Orthologous Groups (COG), respectively, and 46,406 (64.6%) unigenes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 4518 distinct unigenes were observed only inPythium-resistant "Candidum" roots, of which 98 seemed to be involved in disease resistance and defense responses. In addition, 28,837 simple sequence repeat sites and 44,628 single nucleotide polymorphism sites were identified among the three caladium cultivars. These root transcriptome data will be valuable for further genetic improvement of caladium and related aroids.
authors.affiliation: Gulf Coast Research and Education Center, Department of Environmental Horticulture, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA. cjun01@gmail.com.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Cao
authors.affiliation: Gulf Coast Research and Education Center, Department of Environmental Horticulture, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA. zdeng@ufl.edu.
authors.forename: Zhanao
authors.initials: Z
authors.lastname: Deng
mesh_terms: D029064:Araceae / Q000235:genetics* / Q000378:metabolism; D020451:Contig Mapping; D030541:Databases, Genetic; D060467:Disease Resistance / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011775:Pythium / Q000472:pathogenicity*; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant
keywords: Caladium; RNA-Seq; aroid; de novo assembly; defense-related gene; disease resistance gene; root transcriptome