Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway

Abstract Background The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as...

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Autores principales:	Mohammad Ali Mohammadi, Majid Fasihi Harandi, Donald P. McManus, Mehdi Mansouri
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Transcriptomics Echinococcosis Hydatid disease Functional analysis Pepsin Protoscoleces Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/fbf57f1cda6e4af69c431a156e844a67
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spelling	oai:doaj.org-article:fbf57f1cda6e4af69c431a156e844a672021-11-14T12:25:15ZGenome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway10.1186/s13071-021-05067-91756-3305https://doaj.org/article/fbf57f1cda6e4af69c431a156e844a672021-11-01T00:00:00Zhttps://doi.org/10.1186/s13071-021-05067-9https://doaj.org/toc/1756-3305Abstract Background The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. Methods Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. Results At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. Conclusions The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments. Graphical AbstractMohammad Ali MohammadiMajid Fasihi HarandiDonald P. McManusMehdi MansouriBMCarticleTranscriptomicsEchinococcosisHydatid diseaseFunctional analysisPepsinProtoscolecesInfectious and parasitic diseasesRC109-216ENParasites & Vectors, Vol 14, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Transcriptomics Echinococcosis Hydatid disease Functional analysis Pepsin Protoscoleces Infectious and parasitic diseases RC109-216
spellingShingle	Transcriptomics Echinococcosis Hydatid disease Functional analysis Pepsin Protoscoleces Infectious and parasitic diseases RC109-216 Mohammad Ali Mohammadi Majid Fasihi Harandi Donald P. McManus Mehdi Mansouri Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
description	Abstract Background The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. Methods Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. Results At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. Conclusions The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments. Graphical Abstract
format	article
author	Mohammad Ali Mohammadi Majid Fasihi Harandi Donald P. McManus Mehdi Mansouri
author_facet	Mohammad Ali Mohammadi Majid Fasihi Harandi Donald P. McManus Mehdi Mansouri
author_sort	Mohammad Ali Mohammadi
title	Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
title_short	Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
title_full	Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
title_fullStr	Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
title_full_unstemmed	Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
title_sort	genome-wide transcriptome analysis of the early developmental stages of echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway
publisher	BMC
publishDate	2021
url	https://doaj.org/article/fbf57f1cda6e4af69c431a156e844a67
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Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway

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