Transcriptome analysis of dormant tomonts of the marine fish ectoparasitic ciliate Cryptocaryon irritans under low temperature

Abstract

Background: Cryptocaryon irritans, a species of obligatory ciliate ectoparasite, can infect various species of marine teleost fish. Cryptocaryon irritans that fall to the seabed or aquarium bottom in winter can form "dormant tomonts" and wake up when the temperature rises the next year. Abundant studies and analyses on the dormant tomonts were carried out at the transcriptome level, in order to investigate the molecular mechanism of C. irritans tomonts entering the dormant state under low-temperature conditions.

Methods: The paired-end sequencing strategy was used to better assemble the entire transcriptome de novo. All clean sequencing reads from each of the three libraries (Group A: untreated blank control; Group B: treated for 24 h at 12 °C; and Group C: developed for 24 h at 25 °C) were respectively mapped back to the transcriptome assembly using the bioinformatics software.

Results: In this study, 25,695,034, 21,944,467, and 28,722,875 paired-end clean reads were obtained respectively from the three cDNA libraries of the C. irritans tomont by Illumina paired-end sequencing technology. A total of 25,925 unique transcript fragments (unigenes) were assembled, with an average length of 839 bp. Differentially expressed genes (DEGs) were scrutinized; in Group B/A pairwise comparison, 343 genes presented differential expression, including 265 up-regulated genes and 78 down-regulated genes in Group B; in Group C/A pairwise comparison, there were 567 DEGs, including 548 up-regulated genes and 19 down-regulated genes in Group C; and in Group B/C pairwise comparison, 185 genes showed differential expression, including 145 up-regulated genes and 40 down-regulated genes in Group B.

Conclusions: This is the first transcriptomic analytical study of the C. irritans tomonts under low temperature. It can be concluded that most of the genes required for its cell survival under low temperature, or for cell entry into a deeper dormancy state were discovered, and that they might be considered as candidate genes to develop the diagnostic and control measures for cryptocaryoniasis.

Keywords: Cell division; Cryptocaryon irritans; Dormant tomont; Low temperature; Transcriptome.

Fig. 1

Transcriptome sequence length distributions of C. irritans tomont unigenes. The x-axis indicates unigene size and the y-axis indicates the number of unigenes with different lengths

Fig. 2

eggNOG function classification of C. irritans tomonts unigenes. A total of 23,670 hits were classified into 25 categories

Fig. 3

Gene ontology (GO) enrichment analysis of the differently expressed genes in pairwise comparison groups B vs A, B vs C and C vs A. A: untreated blank control, B: treated for 24 h at 12 °C, and C: developed for 24 h at 25 °C

Fig. 4

KEGG pathway enrichment analysis of the differently expressed genes in pairwise comparison groups B vs A, B vs C and C vs A. The x-axis represents KEGG pathway classification and y-axis represents the significance P-value of enrichment in hypergeometric distribution. The red line represents P = 0.05. A: Metabolism; B: Genetic information processing; C: Environmental information processing; D: Cellular processes; E: Organismal systems; F: Human diseases

Fig. 5

Gene list involved in ribosome pathway generated by KEGG of the DEGs in pairwise comparison groups B vs A, B vs C and C vs A. Green indicates significantly increased expression; red, significantly decreased expression; and pink, unchanged expression. Blue denotes genes that were not identified in the expression profile analysis

Fig. 6

Pairwise comparisons of differentially expressed genes in pairwise comparison groups B vs A, B vs C and C vs A. The red, blue, and yellow circles indicate DEGs in groups B vs A, C vs A and B vs C, respectively

Fig. 7

Heat map obtained from the hierarchical clustering of these genes. Shades of red to green represent the up- and down- regulation of genes within each row, where red denotes up-regulation and green denotes down-regulation