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Translational Machinery of Senegalese Sole (Solea senegalensis Kaup) and Atlantic Halibut (Hippoglossus hippoglossus L.): Comparative Sequence Analysis of the Complete Set of 60S Ribosomal Proteins and their Expression

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Abstract

Ribosomal proteins (RPs) comprise a large set of highly evolutionarily conserved proteins that are often over-represented in complementary DNA libraries. They have become very useful markers in comparative genomics, genome evolution, and phylogenetic studies across taxa. In this study, we report the sequences of the complete set of 60S RPs in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species. Amino-acid sequence comparisons of the encoded proteins showed a high similarity both between these two flatfish species and with respect to other fish and human counterparts. Expressed sequence tag analysis revealed the existence of paralogous genes for RPL3, RPL7, RPL41, and RPLP2 in Atlantic halibut and RPL13a in Senegalese sole as well as RPL19 and RPL22 in both species. Phylogenetic analysis of paralogs revealed distinct evolutionary histories for each RP in agreement with three rounds of genome duplications and lineage-specific duplications during flatfish evolution. Steady-state transcript levels for RPL19 and RPL22 RPs were quantitated during larval development and in different tissues of sole and halibut using a real-time polymerase chain reaction approach. All paralogs were expressed ubiquitously although at different levels in different tissues. Most RP transcripts increased coordinately after larval first-feeding in both species but decreased progressively during the metamorphic process. In all cases, expression profiles and transcript levels of orthologous genes in Senegalese sole and Atlantic halibut were highly congruent. The genomic resources and knowledge developed in this survey will be useful for the study of Pleuronectiformes evolution.

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Acknowledgments

This work has been financially supported by Pleurogene project funded by the Genome Canada-Genoma España joint program. Sequencing by the Atlantic Genome Centre (www.tagc.ca), Halifax, Nova Scotia, Canada a partnership between Genome Atlantic and the National Research Council of Canada Institute for Marine Biosciences, is gratefully acknowledged. We thank Dr. Kelly Soanes (IMB) for critical review of this manuscript. This is NRC publication number 2008-42783. MM is the recipient of a research contract from INIA (Spanish Ministry of Science and Technology) cofunded by the European Social Fund.

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  1. IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro de pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain

    Carlos Infante, Jose Pedro Cañavate & Manuel Manchado

  2. Institute for Marine Biosciences, National Research Council, 1411 Oxford Street, Halifax, Nova Scotia, B3H 3Z1, Canada

    Makoto P. Matsuoka, Michael Reith & Susan E. Douglas

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  1. Makoto P. Matsuoka
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  2. Carlos Infante
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  4. Jose Pedro Cañavate
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  6. Manuel Manchado
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Correspondence to Manuel Manchado.

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Matsuoka, M.P., Infante, C., Reith, M. et al. Translational Machinery of Senegalese Sole (Solea senegalensis Kaup) and Atlantic Halibut (Hippoglossus hippoglossus L.): Comparative Sequence Analysis of the Complete Set of 60S Ribosomal Proteins and their Expression. Mar Biotechnol 10, 676–691 (2008). https://doi.org/10.1007/s10126-008-9104-y

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