In this study, we report the first complete mitochondrial genome of the tapeworm Nippotaenia mogurndae in the order Nippotaeniidea Yamaguti, 1939. This mitogenome, which is 14,307 base pairs (bp) long with an A + T content of 72.2%, consists of 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two rRNA genes, and two non-coding regions. Most tRNAs have a conventional cloverleaf structure, but trnS1 and trnR lack dihydrouridine arms of tRNA. The two largest non-coding regions, NCR1 (220 bp) and NCR2 (817 bp), are located between trnY and trnS2 and between nad5 and trnG, respectively. Phylogenetic analyses of mitogenomic data indicate that N. mogurndae is closely related to tapeworms in the order Cyclophyllidea.

Mitochondrial DNA of nematodes undergoes frequent rearrangements, so it is a very good model for studying the mitochondrial genome evolution. The complete mitochondrial genome of a parasitic nematode Senga ophiocephalina was sequenced and annotated. The 13,816 bp-long genome contained 12 protein-coding genes (atp8 gene was missing), two ribosomal RNAs, 22 transfer RNAs, and a 391 bp non-coding region. Phylogenetic analysis showed that S. ophiocephalina forms a monophyletic cluster with the remaining two Bothriocephalidae species.

In the present study, we provide morphological and molecular characterization of two Trichodina species, T. acuta Lom, 1970 and T. funduliWellborn, 1967, isolated from koi (Cyprinus carpio) and loach (Paramisgurnus dabryanus), respectively. Morphological characters of the two Trichodina species were mainly investigated on the basis of dry silver nitrate-impregnated specimens. Both species are medium-sized and possess well-developed denticles comprising strongly sickle-shaped blades, well-developed central parts, and straight rays. Trichodina acuta can be easily distinguished from the other Trichodina species that possess a clear central circle by the well-developed sharp blade apophysis, and the gap between ray tip and central circle. Trichodina funduli is a poorly known species that is easily confused with T. heterodentata Duncan, 1977, however the latter species has thinner denticles. The small subunit ribosomal RNA gene sequences of Trichodina acuta and T. funduli were incorporated into phylogenetic analyses. Our findings suggest that the phylogenetic lineage of trichodinids might not correspond with their living environments, host species or even some morphological characteristics.

Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. In 2015, a provisional species of Clinostomum in People\'s Republic of China (PRC) was distinguished from C. complanatum (Rudolphi, 1819) in Europe based on divergent cytochrome c oxidase I (CO1). However, in subsequent studies in East Asia, the same divergent CO1 genotype was identified as C. complanatum. These matching sequences suggest that either the provisional East Asian species was incorrectly distinguished from C. complanatum in 2015 or that C. complanatum in East Asia was misidentified in later studies. We tested these alternatives by sequencing the mitochondrial genome of C. complanatum in Italy, which was 5.7% divergent from a previously published sequence from Clinostomum in PRC, including differences in 80 of 3390 (2.4%) translated amino acids. Partial CO1 sequences of specimens from PRC and those from Italy, Romania, and Turkey also each formed reciprocally monophyletic clades. Partial CO1 from the East Asian clade varied by mean 3.6% (range 2.4-4.8%) from C. complanatum from Italy, Romania, and Turkey; mean intra-clade CO1 variation was 0.3% (range 0-1.9%). Metacercariae from Europe and East Asia display significant morphometric variation, and data from the literature suggest morphological differences in the genital complex of adults. Although sequences of nuclear rDNA did not differ between isolates from the west and East Asia, taken together, these results lead us to describe a new species of Clinostomum.

Cryptocaryon irritans is an obligate ectoparasitic ciliate pathogen of marine fishes. It can infect most marine teleosts and cause heavy economic losses in aquaculture. There is currently no effective method of controlling this disease, and little information is available regarding the genes involved in its development and virulence. We aimed to investigate the distinct features of the three major life-cycle stages of C. irritans in terms of gene transcription level, and identify candidate vaccines/drug targets. We established a reference transcriptome of C. irritans by RNA-seq.
Three cDNA libraries using total poly(A)+ mRNA isolated from trophonts, tomonts, and theronts was constructed and sequenced, respectively. Clean reads from the three stages were de novo assembled to generated unigene. Annotation of unigenes and transcriptomic comparison of three stages was performed.
Totals of 73.15, 62.23, and 109.57 million clean reads were generated from trophont, tomont, and theront libraries, respectively. After de novo assembly, 49,104 unigenes were obtained, including 9,253 unigenes with significant similarities to proteins from other ciliates. Transcriptomic comparisons revealed that 2,470 genes were differentially expressed among the three stages, including 2,011, 1,404, and 1,797 genes that were significantly differentially expressed in tomont/theront, tomont/trophont, and theront/trophont pairwise comparisons, respectively. Based on the results of hierarchical clustering, all differentially expressed genes (DEGs) were located in five major clusters. DEGs in clusters 1 and 2 were more highly expressed in tomonts than in other stages, DEGs in cluster 3 were dominant in the tomont and trophont stages, whereas clusters 4 and 5 included genes upregulated in the theront stage. In addition, Immobilization antigens (I-antigens) and proteases have long been considered major targets for vaccine development and potential drug targets in parasites, respectively. In the present study, nine putative I-antigens transcripts and 161 protease transcripts were found in the transcriptome of C. irritans.
It was concluded that DEGs enriched in tomonts were involved in cell division, to increase the number of theronts and ensure parasite continuity. DEGs enriched in theronts were associated with response to stimuli, whereas genes enriched in trophonts were related to nutrient accumulation and cell growth. In addition, the I-antigen and protease transcripts in our transcriptome could contribute to the development of vaccines or targeted drugs. Together, the results of the present study provide novel insights into the physiological processes of a marine parasitic ciliate.