Deplazes P, Rinaldi L, Alvarez Rojas CA, Torgerson PR, Harandi MF, Romig T, et al. Global distribution of alveolar and cystic echinococcosis. Adv Parasitol. 2017;95:315–493.
CAS
PubMed
Google Scholar
Borhani M, Fathi S, Darabi E, Jalousian F, Simsek S, Ahmed H, et al. Echinococcoses in Iran, Turkey, and Pakistan: old diseases in the new millennium. Clin Microbiol Rev. 2021;34:e00290-20.
Google Scholar
Thompson RCACA, Jenkins DJJ. Echinococcus as a model system: Biology and epidemiology. Int J Parasitol. 2014;44:865–77.
CAS
PubMed
Google Scholar
Hemphill A, Stadelmann B, Scholl S, Müller J, Spiliotis M, Müller N, et al. Echinococcus metacestodes as laboratory models for the screening of drugs against cestodes and trematodes. Parasitology. 2010;137:569.
CAS
PubMed
Google Scholar
Brehm K, Koziol U. Echinococcus–host interactions at cellular and molecular levels. Adv Parasitol. 2017;95:147–212.
CAS
PubMed
Google Scholar
Thompson RCA, Lymbery AJ. Echinococcus and hydatid disease. Cab International; 1995.
Google Scholar
Thompson RCA. Growth, segmentation and maturation of the British horse and sheep strains of Echinococcus granulosus in dogs. Int J Parasitol. 1977;7:281–5.
CAS
PubMed
Google Scholar
Thompson RCA. Biology and systematics of Echinococcus. In: Echinococcus and Echinococcosis, Part A; 2017. p. 65–109.
Yoshimi A, Abdel-Wahab O. Molecular pathways: understanding and targeting mutant spliceosomal proteins. Clin Cancer Res. 2017;23:336–41.
CAS
PubMed
Google Scholar
Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463:457–63.
CAS
PubMed
PubMed Central
Google Scholar
Will CL, Max RL. Spliceosome structure and function. Cold Spring Harb Perspect Biol. 2002;3:2875–81.
Google Scholar
Wilkinson ME, Charenton C, Nagai K. RNA Splicing by the Spliceosome. Annu Rev Biochem. 2020;89:359–88.
CAS
PubMed
Google Scholar
Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C, Brehm K. A novel terminal-repeat retrotransposon in miniature (TRIM) Is massively expressed in Echinococcus multilocularis stem cells. Genome Biol Evol. 2015;7:2136–53.
CAS
PubMed
PubMed Central
Google Scholar
Yeoh LM, Lee VV, McFadden GI, Ralph SA. Alternative splicing in apicomplexan parasites. MBio Am Soc Microbiol. 2019;10:1–15.
Google Scholar
Koziol U, Brehm K. Recent advances in Echinococcus genomics and stem cell research. Vet Parasitol. 2015;213:92–102.
CAS
PubMed
Google Scholar
Jain P, Karthikeyan C, Hari Narayana Moorthy NS, Kumar Waiker D, Kumar Jain A, Trivedi P. Human CDC2-like kinase 1 (CLK1): a novel target for Alzheimer’s disease. Curr Drug Targets. 2014;15:539–50.
CAS
PubMed
Google Scholar
Sako Y, Ninomiya K, Okuno Y, Toyomoto M, Nishida A, Koike Y, et al. Development of an orally available inhibitor of CLK1 for skipping a mutated dystrophin exon in Duchenne muscular dystrophy. Sci Rep. 2017;7:1–9.
CAS
Google Scholar
Baralle FE, Giudice J. Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol. 2017;18:437–51.
CAS
PubMed
PubMed Central
Google Scholar
Oghabian A. Bioinformatics analysis of intron retention events associated with the minor spliceosome. Helsinki Institute of Life Sciences; 2018.
Google Scholar
Cate JHD. A big bang in spliceosome structural biology. Science (80). 2016;351:1390–2.
CAS
Google Scholar
Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem. 2015;84:165–98.
CAS
PubMed
Google Scholar
Wang Y, Liu J, Huang B, Xu Y-M, Li J, Huang L-F, et al. Mechanism of alternative splicing and its regulation. Biomed Rep. 2014;3:152–8.
PubMed
PubMed Central
Google Scholar
Marzano V, Mancinelli L, Bracaglia G, Del Chierico F, Vernocchi P, Di Girolamo F, et al. “Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”. PLoS Negl Trop Dis. 2017;11:e0005916.
PubMed
PubMed Central
Google Scholar
Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B. A practical comparison of De Novo genome assembly software tools for next-generation sequencing technologies. PLoS ONE. 2011;6:e17915.
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
CAS
PubMed
PubMed Central
Google Scholar
Zhao S, Zhang B, Zheng Z., Zhang T., Zhao S, Zhang B. Impact of gene annotation on RNA-seq data analysis. Next generation sequencing applications and challenges. 2016. p. 428–48.
Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, et al. Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. EvoDevo. 2018;9:1–29.
Google Scholar
Strange RM, Russelburg LP, Delaney KJ. Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes. Genetica. 2016;144:487–96.
CAS
PubMed
Google Scholar
Brehm K, Jensen K, Frosch M. mRNA trans-splicing in the human parasitic cestode Echinococcus multilocularis. J Biol Chem. 2000;275:38311–8.
CAS
PubMed
Google Scholar
Bretagne S, Robert B, Vidaud D, Goossens M, Houin R. Structure of the Echinococcus multilocularis U1 snRNA gene repeat. Mol Biochem Parasitol. 1991;46:285–92.
CAS
PubMed
Google Scholar
Liu S, Zhou X, Hao L, Piao X, Hou N, Chen Q. Genome-Wide transcriptome analysis reveals extensive alternative splicing events in the protoscoleces of Echinococcus granulosus and Echinococcus multilocularis. Front Microbiol. 2017;8:1–14.
Google Scholar
Bowles J, McManus DP, Bowles J, McManus DP. Rapid discrimination of Echinococcus species and strains using a polymerase chain reaction-based RFLP method. Mol Biochem Parasitol. 1993;57:231–9.
CAS
PubMed
Google Scholar
Debarba JA, Sehabiague MPC, Monteiro KM, Gerber AL, Vasconcelos ATR, Ferreira HB, et al. Transcriptomic analysis of the early strobilar development of Echinococcus granulosus. Pathogens. 2020;9:465.
CAS
PubMed Central
Google Scholar
Debarba JA, Monteiro KM, Moura H, Barr JR, Ferreira HB, Zaha A. Identification of newly synthesized proteins by Echinococcus granulosus Protoscoleces upon induction of strobilation. PLoS Negl Trop Dis. 2015;9:1–18.
Google Scholar
FastQC: a quality control tool for high throughput sequence data. Babraham Bioinforma; 2010. http://www.bioinformatics.babraham.ac.uk.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
CAS
PubMed
PubMed Central
Google Scholar
Shen S, Park JW, Lu Z, Lin L, Henry MD, Wu YN, et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014;111:E5593–601.
CAS
PubMed
PubMed Central
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
CAS
PubMed
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6.
CAS
PubMed
Google Scholar
Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, et al. AgriGO v2.0: A GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 2017;45:W122–9.
CAS
PubMed
PubMed Central
Google Scholar
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
PubMed
PubMed Central
Google Scholar
Tokheim C, Park JW, Xing Y. PrimerSeq: design and visualization of RT-PCR primers for alternative splicing using RNA-seq data. Genomics Proteomics Bioinform. 2014;12:105–9.
Google Scholar
Kalsotra A, Cooper TA. Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet. 2011;12:715–29.
CAS
PubMed
PubMed Central
Google Scholar
Lunghi M, Spano F, Magini A, Emiliani C, Carruthers VB, Di Cristina M. Alternative splicing mechanisms orchestrating post-transcriptional gene expression: intron retention and the intron-rich genome of apicomplexan parasites. Curr Genet. 2016;62:31–8.
CAS
PubMed
Google Scholar
Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc B Biol Sci. 2017;372:1–7.
Google Scholar
Thompson RCA, McManus D. Aetiology: parasites and life-cycles. World Organization for Animal Health; 2001. p. 1–19.
Google Scholar
Bai Y, Zhang Z, Jin L, Zhu Y, Zhao L, Shi B, et al. Dynamic changes in the global transcriptome and MicroRNAome reveal complex miRNA-mRNA regulation in early stages of the bi-directional development of Echinococcus granulosus Protoscoleces. Front Microbiol. 2020;11:1–15.
CAS
Google Scholar
Piao X, Hou N, Cai P, Liu S, Wu C, Chen Q. Genome-wide transcriptome analysis shows extensive alternative RNA splicing in the zoonotic parasite Schistosoma japonicum. BMC Genomics. 2014;15:1–12.
Google Scholar
Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, et al. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res. 2011;21:342–8.
CAS
PubMed
PubMed Central
Google Scholar
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 2011;471:473–9.
CAS
PubMed
Google Scholar
Kashyap L, Sharma RK. Alternative splicing: a paradoxical qudo in eukaryotic genomes. Bioinformation. 2012;2:155–6.
Google Scholar
Carmel L, Wolf YI, Rogozin IB, Koonin EV. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res. 2007;17:1034–44.
CAS
PubMed
PubMed Central
Google Scholar
Kenyon C. A pathway that links reproductive status to lifespan in Caenorhabditis elegans. Ann N Y Acad Sci. 2010;1204:156–62.
CAS
PubMed
Google Scholar
Wang X, Xu X, Lu X, Zhang Y, Pan W. Transcriptome bioinformatical analysis of vertebrate stages of Schistosoma japonicum reveals alternative splicing events. Zheng Z-M, editor. PLoS One. 2015;10:1–17.
Shen S, Park JW, Huang J, Dittmar KA, Lu Z, Zhou Q, et al. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res. 2012;40:e61–e61.
CAS
PubMed
PubMed Central
Google Scholar
DeMarco R, Oliveira KC, Venancio TM, Verjovski-Almeida S. Gender biased differential alternative splicing patterns of the transcriptional cofactor CA150 gene in Schistosoma mansoni. Mol Biochem Parasitol. 2006;150:123–31.
CAS
PubMed
Google Scholar
Fan J, Wu H, Li K, Liu X, Tan Q, Cao W, et al. Transcriptomic analysis of the Echinococcus granulosus protoscolex in the encystation process. Korean J Parasitol. 2020;58:287–99.
CAS
PubMed
PubMed Central
Google Scholar
Ghazi A, Henis-Korenblit S, Kenyon C. A transcription elongation factor that links signals from the reproductive system to lifespan extension in Caenorhabditis elegans. PLoS Genet. 2009;5:e1000639.
PubMed
PubMed Central
Google Scholar
Mori N, Mook-Jung I. Aging mechanisms: Longevity, metabolism, and brain aging. Springer; 2015.
Google Scholar
Hemer S, Konrad C, Spiliotis M, Koziol U, Schaack D, Förster S, et al. Host insulin stimulates Echinococcus multilocularis insulin signalling pathways and larval development. BMC Biol. 2014;12:1–22.
Google Scholar
Romig T, Deplazes P, Jenkins D, Giraudoux P, Massolo A, Craig PS, et al. Ecology and life cycle patterns of Echinococcus species. Adv Parasitol. 2017;95:213–314.
CAS
PubMed
Google Scholar
Liang J, Wen J, Huang Z, Chen X, Zhang B, Chu L. Small nucleolar RNAs: insight into their function in cancer. Front Oncol. 2019;9:587.
PubMed
PubMed Central
Google Scholar
Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, et al. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007;13:1923–39.
CAS
PubMed
PubMed Central
Google Scholar
Hull R, Dlamini Z. The role played by alternative splicing in antigenic variability in human endo-parasites. Parasit Vectors. 2014;7:1–19.
Google Scholar
Effenberger KA, Urabe VK, Jurica MS. Modulating splicing with small molecular inhibitors of the spliceosome. Wiley Interdiscip Rev RNA. 2017;8:e1381.
Google Scholar
Berriman M, Haas BJ, Loverde PT, Wilson RA, Dillon GP, Cerqueira GC, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 2009;460:352–8.
CAS
PubMed
PubMed Central
Google Scholar