The complete mitochondrial genome of the tapeworm Cladotaenia vulturi (Cestoda: Paruterinidae): gene arrangement and phylogenetic relationships with other cestodes

Table S1. Primers used for amplifying mtDNA fragments and their positions in the mt genome of Cladotaenia vulturi. (DOC 30 kb

Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium

Background Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Results Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Conclusion Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets

Transcriptome Analysis in Chicken Cecal Epithelia upon Infection by Eimeria tenella In Vivo

Coccidiosis, caused by various Eimeria species, is a major parasitic disease in chickens. However, our understanding on how chickens respond to coccidian infection is highly limited at both molecular and cellular levels. The present study employed the Affymetrix chicken genome array and performed transcriptome analysis on chicken cecal epithelia in response to infection for 4.5 days in vivo by the cecal-specific species E. tenella. By Significance Analysis of Microarrays (SAM), we have identified 7,099 probe sets with q-values at <0.05, in which 4,033 and 3,066 genes were found to be up- or down-regulated in response to parasite infection. The reliability of the microarray data were validated by real-time qRT-PCR of 20 genes with varied fold changes in expression (i.e., correlation coefficient between microarray and qRT-PCR datasets: R (2) = 0.8773, p<0.0001). Gene ontology analysis, KEGG pathway mapping and manual annotations of regulated genes indicated that up-regulated genes were mainly involved in immunity/defense, responses to various stimuli, apoptosis/cell death and differentiation, signal transduction and extracellular matrix (ECM), whereas down-regulated genes were mainly encoding general metabolic enzymes, membrane components, and some transporters. Chickens mustered complex cecal eipthelia molecular and immunological responses in response to E. tenella infection, which included pathways involved in cytokine production and interactions, natural killer cell mediated cytotoxicity, and intestinal IgA production. In response to the pathogenesis and damage caused by infection, chicken cecal epithelia reduced general metabolism, DNA replication and repair, protein degradation, and mitochondrial functions

Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica

Comparative Analysis of Cystatin Superfamily in Platyhelminths

<div><p>The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG) was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW), a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of <i>Taenia solium</i> cystatin, one of the cestode cystatins, demonstrated that the N-terminus of <i>T</i>. <i>solium</i> cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in <i>T</i>. <i>solium</i> cystatin, the models of <i>T</i>. <i>solium</i> cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that <i>T</i>. <i>solium</i> cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of <i>T</i>. <i>solium</i> cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution.</p></div

Additional file 1:Table S1. of The complete mitochondrial genome of Anoplocephala perfoliata, the first representative for the family Anoplocephalidae

Cestode species used for comparative analysis with Anoplocephala. perfoliata. Table S2. A + T content (%) of the protein-coding, tRNA, rRNA genes and non-coding regions of mitochondrial genome of Anoplocephala perfoliata. Table S3. Properties of mtDNA protein-coding genes, rRNA genes and non-coding regions of Anoplocephala perfoliata and other cestode species. Table S4. Primers used to amplify and sequence mitochondrial genome from Anoplocephala perfoliata. (DOC 209 kb

Additional file 1: of Characterization of the complete mitochondrial genome of the cloacal tapeworm Cloacotaenia megalops (Cestoda: Hymenolepididae)

Table S1. Primers used to amplify PCR fragments for Cloacotaenia megalops. (DOC 37 kb

The complete mitochondrial genome of Anoplocephala perfoliata, the first representative for the family Anoplocephalidae

Abstract Background Mitochondrial (mt) genome sequences are widely used to understand phylogenetic relationships among parasites. However, no complete mt genome sequence is available in the family Anoplocephalidae to date. This study sequenced and annotated the complete mt genome of Anoplocephala perfoliata (Anoplocephalidae), and investigated its phylogenetic relationships with other species from the families Hymenolepididae, Dipylidiidae and Taeniidae of the order Cyclophyllidea using the amino acid sequences of the 12 proteins in their mt genomes. Methods The complete mt genome of A. perfoliata was amplified by Long-range PCR, sequenced using primer walking and annotated by comparing with those of other cestodes. Its phylogenetic relationship with the species from the families Hymenolepididae, Dipylidiidae and Taeniidae was inferred using the 12 protein sequences based on Maximum likelihood and Bayesian methods. Results The complete circular mt genome sequence for A. perfoliata is 14,459 bp in size, and includes 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The mt gene arrangement of A. perfoliata is identical to those of previously reported Hymenolepis diminuta (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but slightly different from those of other taeniids due to an order switch between tRNA(S2) and tRNA(L1). The phylogenetic analyses showed that the Dipylidiidae was more closely related to Anoplocephalidae and Hymenolepididae than to Taeniidae. The relationship among the four families obtained by Maximum likelihood and Bayesian inferences based on predicted amino acid sequences of protein-coding genes is consistent with that based on their mt gene arrangement similarities. Conclusions This study determined the first mt genome for the family Anoplocephalidae, providing rich sources for selecting useful molecular markers for ecological and phylogenetic studies. Analyses on mt genome sequences of the four families of cestodes provide novel insights into their phylogenetic relationships. Of couse, more taxon sampling is necessary for future phylogenetic studies of these cestodes using mt genome sequences