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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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Phylogenetic tree of Crybb and Crybb-like proteins in vertebrates. A neighbor-joining tree based on the alignment of vertebrates Crybb and Crybb-like sequences was built. Species are indicated as Sse (Solea senegalensis), Sso (Solea solea) Dre (Danio rerio), Tni (Tetraodon nigroviridis), Oni (Oreochromis niloticus), Ola (Oryzia slatipes), Cse (Cynoglossus semilaevis), Xla (Xenopus laevis) and Gga (Gallus gallus; see Additional file 7 for accession numbers). Solea sequences are indicated according to the transcript name assigned in SoleaDB. Clusters are indicated as arcs of a circle. The tree obtained was rooted using Xenopus laevis Cryga. Numbers adjacent to nodes indicate percentage bootstrap support; only values larger than 70% (over 1,000 replicates) are shown.
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Fig6: Phylogenetic tree of Crybb and Crybb-like proteins in vertebrates. A neighbor-joining tree based on the alignment of vertebrates Crybb and Crybb-like sequences was built. Species are indicated as Sse (Solea senegalensis), Sso (Solea solea) Dre (Danio rerio), Tni (Tetraodon nigroviridis), Oni (Oreochromis niloticus), Ola (Oryzia slatipes), Cse (Cynoglossus semilaevis), Xla (Xenopus laevis) and Gga (Gallus gallus; see Additional file 7 for accession numbers). Solea sequences are indicated according to the transcript name assigned in SoleaDB. Clusters are indicated as arcs of a circle. The tree obtained was rooted using Xenopus laevis Cryga. Numbers adjacent to nodes indicate percentage bootstrap support; only values larger than 70% (over 1,000 replicates) are shown.

Mentions: Recently, it has been suggested that the visual system had evolved in relation to their benthic way of life [26]. This observation is based on the loss of genes related with vision such as crystallins crybb2 and crybb3 in C. semilaevis[26]. Five crybb orthologs have been identified in S. senegalensis and S. solea transcriptomes that grouped into crybb1 and crybb3 clusters (with two distinct crybb3-encoding transcripts in S. solea similarly to T. nigroviridis) and none to the crybb2 clade (Figure 6 and Additional file 7). Moreover, additional crybb-like transcripts could be grouped into two crybb1-related clusters that seem to be fish-specific sequences. Extension of the analysis to closely related crybb-like sequences revealed that additional crybb sequences exist in all three flatfish C. semilaevis (two sequences), S. solea (two sequences) and S. senegalensis (four sequences). Moreover, EST sequence analysis from Atlantic halibut (Hippoglossus hippoglossus) suggested that this flatfish also possesses crybb1, crybb2 and several crybb1-like sequences (X. Cousin, personal communication). Taken together these results suggest that flatfish have indeed lost and retained specifically some crybb genes likely as a consequence of independent events indicative of divergent evolution and do not support a decay of the visual system as previously hypothesized in flatfish based on the set of crystallin-encoding genes [26].Figure 6


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)

Phylogenetic tree of Crybb and Crybb-like proteins in vertebrates. A neighbor-joining tree based on the alignment of vertebrates Crybb and Crybb-like sequences was built. Species are indicated as Sse (Solea senegalensis), Sso (Solea solea) Dre (Danio rerio), Tni (Tetraodon nigroviridis), Oni (Oreochromis niloticus), Ola (Oryzia slatipes), Cse (Cynoglossus semilaevis), Xla (Xenopus laevis) and Gga (Gallus gallus; see Additional file 7 for accession numbers). Solea sequences are indicated according to the transcript name assigned in SoleaDB. Clusters are indicated as arcs of a circle. The tree obtained was rooted using Xenopus laevis Cryga. Numbers adjacent to nodes indicate percentage bootstrap support; only values larger than 70% (over 1,000 replicates) are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Phylogenetic tree of Crybb and Crybb-like proteins in vertebrates. A neighbor-joining tree based on the alignment of vertebrates Crybb and Crybb-like sequences was built. Species are indicated as Sse (Solea senegalensis), Sso (Solea solea) Dre (Danio rerio), Tni (Tetraodon nigroviridis), Oni (Oreochromis niloticus), Ola (Oryzia slatipes), Cse (Cynoglossus semilaevis), Xla (Xenopus laevis) and Gga (Gallus gallus; see Additional file 7 for accession numbers). Solea sequences are indicated according to the transcript name assigned in SoleaDB. Clusters are indicated as arcs of a circle. The tree obtained was rooted using Xenopus laevis Cryga. Numbers adjacent to nodes indicate percentage bootstrap support; only values larger than 70% (over 1,000 replicates) are shown.
Mentions: Recently, it has been suggested that the visual system had evolved in relation to their benthic way of life [26]. This observation is based on the loss of genes related with vision such as crystallins crybb2 and crybb3 in C. semilaevis[26]. Five crybb orthologs have been identified in S. senegalensis and S. solea transcriptomes that grouped into crybb1 and crybb3 clusters (with two distinct crybb3-encoding transcripts in S. solea similarly to T. nigroviridis) and none to the crybb2 clade (Figure 6 and Additional file 7). Moreover, additional crybb-like transcripts could be grouped into two crybb1-related clusters that seem to be fish-specific sequences. Extension of the analysis to closely related crybb-like sequences revealed that additional crybb sequences exist in all three flatfish C. semilaevis (two sequences), S. solea (two sequences) and S. senegalensis (four sequences). Moreover, EST sequence analysis from Atlantic halibut (Hippoglossus hippoglossus) suggested that this flatfish also possesses crybb1, crybb2 and several crybb1-like sequences (X. Cousin, personal communication). Taken together these results suggest that flatfish have indeed lost and retained specifically some crybb genes likely as a consequence of independent events indicative of divergent evolution and do not support a decay of the visual system as previously hypothesized in flatfish based on the set of crystallin-encoding genes [26].Figure 6

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
Related in: MedlinePlus