title: De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.
abstract: The protistan parasite Perkinsus olseni is a deadly causative agent of perkinsosis, a molluscan disease affecting Manila clam (Ruditapes philippinarum), having a significant impact on world mollusc production. Deciphering the underlying molecular mechanisms in R. philippinarum-P. olseni interaction is crucial for controlling this parasitosis. The present study investigated the transcriptional expression in the parasite trophozoite using RNA-seq. Control and treatment (in vitro challenged with Manila clam-plasma) P. olseni trophozoite RNA were extracted and sequenced on the Illumina HiSeq 2000 instrument using a 100-bp paired-end sequencing strategy. Paired reads (64.7 million) were de novo assembled using Trinity, and the resultant transcripts were further clustered using CAP3. The re-constructed P. olseni transcriptome contains 47,590 unique transcripts of which 23,505 were annotated to 9764 unique proteins. A large number of genes were associated with Gene Ontology terms such as stress and immune-response, cell homeostasis, antioxidation, cell communication, signal transduction, signalling and proteolysis. Among annotated transcripts, a preliminary gene expression analysis detected 679 up-regulated and 478 down-regulated genes, linked to virulence factors, anti-oxidants, adhesion and immune-response molecules. Genes of several metabolic pathways such as DOXP/MEP, FAS II or folate biosynthesis, which are potential therapeutic targets, were identified. This study is the first description of the P. olseni transcriptome, and provides a substantial genomic resource for studying the molecular mechanisms of the host-parasite interaction in perkinsosis. In this sense, it is also the first evaluation of the parasite gene expression after challenge with clam extracellular products.
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain; Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna 9208, Bangladesh.
authors.forename: Abul Farah Md
authors.initials: AF
authors.lastname: Hasanuzzaman
authors.affiliation: Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Robledo
authors.affiliation: Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Gómez-Tato
authors.affiliation: Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Jose A
authors.initials: JA
authors.lastname: Alvarez-Dios
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom.
authors.forename: Peter W
authors.initials: PW
authors.lastname: Harrison
authors.affiliation: Centro de Investigacións Mariñas (CIMA), Consellería do Medio Rural e do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
authors.forename: Asunción
authors.initials: A
authors.lastname: Cao
authors.affiliation: Centro de Investigacións Mariñas (CIMA), Consellería do Medio Rural e do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
authors.forename: Sergio
authors.initials: S
authors.lastname: Fernández-Boo
authors.affiliation: Centro de Investigacións Mariñas (CIMA), Consellería do Medio Rural e do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Villalba
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain. Electronic address: belen.gomez@usc.es.
authors.forename: Belén G
authors.initials: BG
authors.lastname: Pardo
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Paulino
authors.initials: P
authors.lastname: Martínez
mesh_terms: D056893:Alveolata / Q000235:genetics* / Q000472:pathogenicity; D000604:Amino Acyl-tRNA Synthetases / Q000378:metabolism; D000818:Animals; D049872:Bivalvia / Q000469:parasitology*; D005492:Folic Acid / Q000096:biosynthesis; D005786:Gene Expression Regulation; D006458:Hemolymph / Q000737:chemistry; D006790:Host-Parasite Interactions / Q000235:genetics*; D008055:Lipids / Q000096:biosynthesis / Q000235:genetics; D010447:Peptide Hydrolases / Q000378:metabolism; D011480:Protease Inhibitors / Q000378:metabolism; D011743:Pyrimidines / Q000096:biosynthesis; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D053058:Trophozoites / Q000502:physiology*; D037521:Virulence Factors / Q000502:physiology
chemical_list: D008055:Lipids; D011480:Protease Inhibitors; D011743:Pyrimidines; D037521:Virulence Factors; D012313:RNA; D005492:Folic Acid; D010447:Peptide Hydrolases; D000604:Amino Acyl-tRNA Synthetases; C030986:pyrimidine
keywords: Gene expression; Pathogenicity; Perkinsus olseni; RNA-seq; Response to host-immunity; Transcriptome