Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform.
BACKGROUND
The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species.


RESULTS
Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data.


CONCLUSIONS
New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.
Cerdà
Joan
J
Laboratory of the Institut de Recerca i Tecnologia Agroalimentàries-Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, 08003 Barcelona, Spain. joan.cerda@irta.es
Mercadé
Jaume
J
Lozano
Juan José
JJ
Manchado
Manuel
M
Tingaud-Sequeira
Angèle
A
Astola
Antonio
A
Infante
Carlos
C
Halm
Silke
S
Viñas
Jordi
J
Castellana
Barbara
B
Asensio
Esther
E
Cañavate
Pedro
P
Martínez-Rodríguez
Gonzalo
G
Piferrer
Francesc
F
Planas
Josep V
JV
Prat
Francesc
F
Yúfera
Manuel
M
Durany
Olga
O
Subirada
Francesc
F
Rosell
Elisabet
E
Maes
Tamara
T
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D020224:Expressed Sequence Tags; D005412:Flatfishes / Q000235:genetics*; D015723:Gene Library; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods