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. 2017 Mar 27;18(4):712.
doi: 10.3390/ijms18040712.

De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes

Zhe Cao  1 , Zhanao Deng  2
Affiliations

De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes

Zhe Cao et al. Int J Mol Sci. .

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 to Pythiummyriotylum, 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 in Pythium-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.

Keywords: Caladium; RNA-Seq; aroid; de novo assembly; defense-related gene; disease resistance gene; root transcriptome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Characterization of caladium unigenes via similarity searches against the NR database. (A) E-value distribution of BLAST hits for the assembled unigenes; (B) similarity distribution of BLAST hits for the assembled unigenes; and (C) species distribution of the top BLAST hits for the assembled unigenes.
Figure 2
Figure 2
Gene ontology (GO) classification of annotated caladium unigenes. Results were grouped into three main categories: Biological Process, Cellular Component, and Molecular Function. The right y-axis showed the number of unigenes corresponding to each subcategory, and the left y-axis showed the percentage of unigenes involved in each specific subcategory.
Figure 3
Figure 3
Root-specific unigenes identified in the three caladium root transcriptomes. The y-axis on the right indicates the functional annotation categories, and the x-axis on the bottom shows the number of unigenes falling into each functional annotation category.
Figure 4
Figure 4
Clusters of Orthologous Groups (COG) classification of assembled caladium unigenes. The COG function classification of these unigenes fell into 26 categories (x-axis). The y-axis showed the number of caladium unigenes corresponding to each category.
Figure 5
Figure 5
Length distribution of CDS predicted in the NR, Swiss-prot, KEGG and COG databases (A), or by the ESTscan (B).
Figure 6
Figure 6
Venn diagram showing the number of specific and common unigenes in three caladium cultivars, “Candidum”, “Gingerland”, and “Miss Muffet”.
See this image and copyright information in PMC

References

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