Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.
The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species.
Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: belen.gomez@usc.es.
Belén G
BG
Pardo
Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15781 Santiago de Compostela, Spain. Electronic address: joseantonio.alvarez.dios@usc.es.
José Antonio
JA
Álvarez-Dios
Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain. Electronic address: asuncion.cao.hermida@xunta.gal.
Asunción
A
Cao
Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain. Electronic address: andrea.ramilo.alvarez@xunta.es.
Andrea
A
Ramilo
Departamento de Matemáticas, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain. Electronic address: antonio.gomez.tato@usc.es.
Antonio
A
Gómez-Tato
Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08007, Barcelona, Spain. Electronic address: jplanas@ub.edu.
Josep V
JV
Planas
Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871 Alcalá de Henares, Spain. Electronic address: antonio.villalba.garcia@xunta.gal.
Antonio
A
Villalba
Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: paulino.martinez@usc.es.
Paulino
P
Martínez
D000818:Animals; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D016678:Genome; D041602:Haplosporida / Q000276:immunology*; D006434:Hemocytes / Q000276:immunology / Q000378:metabolism / Q000469:parasitology; D007113:Immunity, Innate; D020411:Oligonucleotide Array Sequence Analysis; D049895:Ostrea / Q000235:genetics* / Q000276:immunology / Q000469:parasitology*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D059467:Transcriptome
Bonamiosis; Database; Flat oyster; Genome; Haemocytes; Immune response; NGS; Oligo-microarray; Transcriptome