De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Caladium (Caladium ×hortulanum)

Caladium (Caladium ×hortulanum Birdsey), a member of the Araceae (aroid) family, is an important foliage plant used in pots, hanging baskets and landscapes. The great majority of commercial caladium plants are forced from tubers. Pythium root rot is a major disease affecting caladium root health and tuber yield and quality. Improving caladium resistance to Pythium root rot has become an important objective in caladium breeding. Previous studies have shown the existence of moderate levels of difference among caladium cultivars in Pythium root rot resistance. The objective of this study was to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars with different levels of Pythium root rot resistance, using the high throughput sequencing platform Illumina HiSeq2000. Forty-six to 61 million clean sequence reads were obtained for the root transcriptome of ‘Candidum’ (CDD; moderately resistant to Pythium root rot), ‘Gingerland’ (GGL; highly susceptible to Pythium root rot) and ‘Miss Muffet’ (MFT; highly susceptible to Pythium root rot). De novoassembly of these reads generated approximately 130,000 unigenes, with an N50 length of 1,755 bp. Based on sequence similarity search with known proteins, 71,825 (52.3%) genes were identified and annotated against the NCBI non-redundant protein and Swiss-Prot databases. Out of these annotated unigenes, 48,417 (67.4%), and 31,417 (72.7%) were assigned to gene ontology (GO) and clusters of orthologous group (COG), respectively. In addition, 46,406 (64.6%) genes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among the primary KEGG categories, metabolism was the largest category (12,474, 26.88%), indicating that active metabolic process in caladium roots. A total of 17,755 and 14,902 unigenes were differentially expressed (DE) between CCD and GGL, and CCD and MFT, respectively; 182 of these DE unigenes seemed to be involved in plant disease resistance or defense response processes. By using unigenes as reference, 28,837 simple sequence repeat (SSR) sites were identified, and the most dominant type was dinucleotide repeats (15,504; 53.8%). A search for single nucleotide polymorphisms (SNPs) identified 44,628 SNPs; the most abundant SNPs were transition-type (about 60.1%) of cytosine to thymine (C-T) or adenine to guanine (A-G). The information of assembled transcriptome, identified SSR and SNPs markers in this study could serve as an important foundation for further genomics studies in caladium as well as other species in the Araceae family.