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De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray.

Benzekri H, Armesto P, Cousin X, Rovira M, Crespo D, Merlo MA, Mazurais D, Bautista R, Guerrero-Fernández D, Fernandez-Pozo N, Ponce M, Infante C, Zambonino JL, Nidelet S, Gut M, Rebordinos L, Planas JV, Bégout ML, Claros MG, Manchado M - BMC Genomics (2014)

Bottom Line: Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR.The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies.Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

View Article: PubMed Central - PubMed

Affiliation: IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain. manuel.manchado@juntadeandalucia.es.

ABSTRACT

Background: Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution.

Results: A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB.

Conclusions: Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

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Schematic representation of the probe selection strategy for the construction of the Senegalese sole oligonucleotide microarray. The number of transcripts that resulted after the described filtration is indicated.
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Fig7: Schematic representation of the probe selection strategy for the construction of the Senegalese sole oligonucleotide microarray. The number of transcripts that resulted after the described filtration is indicated.

Mentions: Microarrays have become a cost-effective technique for gene expression profiling and whole-transcriptome studies [7]. Two species-specific oligo-DNA microarrays have been reported in S. senegalensis and S. solea containing a limited number of unique transcripts due to the limited number of ESTs available in soles [19, 20]. This limitation was compensated to some extent using heterologous microarrays [49]. The sole transcriptomes described in this study have overcome these restrictions. The strategy to select sole-specific probes is depicted in Figure 7. Briefly, the 5,545 complete non-redundant transcripts were added to the 34,291 longest, non-redundant, incomplete transcripts. Clustering them resulted in 30,119 longest, non-redundant transcripts (Figure 7) that were combined with 13,284 selected “Coding” transcripts, providing a total of 43,303 probes. The final panel of probes included genes related to reproduction, cell differentiation, response to stress, growth, biosynthetic and catabolic processes, transport, embryonic development and immune system, among other functions.Figure 7


De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray.

Benzekri H, Armesto P, Cousin X, Rovira M, Crespo D, Merlo MA, Mazurais D, Bautista R, Guerrero-Fernández D, Fernandez-Pozo N, Ponce M, Infante C, Zambonino JL, Nidelet S, Gut M, Rebordinos L, Planas JV, Bégout ML, Claros MG, Manchado M - BMC Genomics (2014)

Schematic representation of the probe selection strategy for the construction of the Senegalese sole oligonucleotide microarray. The number of transcripts that resulted after the described filtration is indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4232633&req=5

Fig7: Schematic representation of the probe selection strategy for the construction of the Senegalese sole oligonucleotide microarray. The number of transcripts that resulted after the described filtration is indicated.
Mentions: Microarrays have become a cost-effective technique for gene expression profiling and whole-transcriptome studies [7]. Two species-specific oligo-DNA microarrays have been reported in S. senegalensis and S. solea containing a limited number of unique transcripts due to the limited number of ESTs available in soles [19, 20]. This limitation was compensated to some extent using heterologous microarrays [49]. The sole transcriptomes described in this study have overcome these restrictions. The strategy to select sole-specific probes is depicted in Figure 7. Briefly, the 5,545 complete non-redundant transcripts were added to the 34,291 longest, non-redundant, incomplete transcripts. Clustering them resulted in 30,119 longest, non-redundant transcripts (Figure 7) that were combined with 13,284 selected “Coding” transcripts, providing a total of 43,303 probes. The final panel of probes included genes related to reproduction, cell differentiation, response to stress, growth, biosynthetic and catabolic processes, transport, embryonic development and immune system, among other functions.Figure 7

Bottom Line: Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR.The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies.Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

View Article: PubMed Central - PubMed

Affiliation: IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain. manuel.manchado@juntadeandalucia.es.

ABSTRACT

Background: Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution.

Results: A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB.

Conclusions: Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

Show MeSH