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Título

Building on the transcriptome of gilthead sea bream (Sparus aurata). De novo assembly of next-generation sequencing data

Autor Calduch-Giner, Josep A. ; Borrel-Roda, Miriam ; Pérez-Sánchez, Jaume
Fecha de publicación 4-jun-2012
EditorInternational Symposium on Nutrition and Feeding in Fish
Citación XV International Symposium on Fish Nutrition and Feeding (2012)
ResumenThe gilthead sea bream (GSB) is the main teleost species cultured in the Mediterranean area and during the last decade more than 1,200 scientific papers have been published on GSB nutrition, physiology and genetics. This high valuable fish for aquaculture industry becomes, thereby, an interesting model species for research. In particular, how nutrients modulate fish performance has been explored already, but integrative tools are still limited, and a major goal of our research group in ongoing European projects (AQUAEXCEL, ARRAINA) is to integrate new genomic data in reference database repositories to assist fish phenotyping and the development of biomarker panels of prognostic and diagnostic value. Thus far, the public NCBI database contains 1,733 nucleotide sequence records and 74,877 expressed sequence tags (ESTs) of GSB, mostly derived from AQUAFIRST EU project and the Consortium of Marine Genomics Europe. Additional ESTs (8,754) derived from the AQUAMAX EU project come from suppressive subtraction hybridization (SSH) libraries of fish with signs of essential fatty acid deficiencies. Now, further improvement of GSB transcriptome has been made by means of next-generation sequencing (454 pyrosequencing) that enable the generation of millions of sequences in a single run. This approach included the construction of five normalized 454 libraries from metabolically and immunologically relevant tissues (muscle, intestine, head kidney, blood). A total of 2,945,914 high-quality reads with an average length of 313 nt were produced and de novo assembly of new and public reads was performed by the Sigenae bio-informatic platform (INRA, Toulouse, France). The assembled sequences are hosted in a private database (www.sigenae.org/iats) that is composed of 125,263 unique sequences with an average length of 727 nt. BlastX analysis directed to Swissprot database allowed the annotation of 45,449 sequences (average length of 954 nt), encoding 12,590 different genes. This number of annotated sequences is equivalent to that reported in the Ensembl genome database for Atlantic cod (Gadus morhua) and fish model species, such as the three-spined stickleback (Gasterosteus aculeatus). Besides, when blasting randomly selected stickleback transcripts (n=200) against the GSB database, almost all annotated (E-value < 5e-20) and non-annotated (E-value < 2e-09) sequences had a significant annotated hit. These findings highlight the high quality of GSB transcriptome database, probably containing more than 75% of actively transcribed genes. This constitutes a valuable genomic resource to assist the discovery of new biomarkers that precede the onset of metabolic disturbances to predict the capacity of the animal to cope with nutritional, developmental and environmental-related stressors.
Descripción Póster presentado en el XV International Symposium on Fish Nutrition and Feeding celebrado en Molde (Noruega) del 4 al 7 de junio de 2012.
URI http://hdl.handle.net/10261/89877
Aparece en las colecciones: (IATS) Comunicaciones congresos
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