Genetic characterization of Plectorhinchus mediterraneus yields important clues about genome organization and evolution of multigene families

Manuel A Merlo,Ismael Cross,Manuel Manchado,Laureana Rebordinos,Silvia Portela-Bens,Tiziana Pacchiarini

doi:10.1186/1471-2156-13-33

Abstract

BackgroundMolecular and cytogenetic markers are of great use for to fish characterization, identification, phylogenetics and evolution. Multigene families have proven to be good markers for a better understanding of the variability, organization and evolution of fish species. Three different tandemly-repeated gene families (45S rDNA, 5S rDNA and U2 snDNA) have been studied in Plectorhinchus mediterraneus (Teleostei: Haemulidae), at both molecular and cytogenetic level, to elucidate the taxonomy and evolution of these multigene families, as well as for comparative purposes with other species of the family.ResultsFour different types of 5S rDNA were obtained; two of them showed a high homology with that of Raja asterias, and the putative implication of a horizontal transfer event and its consequences for the organization and evolution of the 5S rDNA have been discussed. The other two types do not resemble any other species, but in one of them a putative tRNA-derived SINE was observed for the first time, which could have implications in the evolution of the 5S rDNA. The ITS-1 sequence was more related to a species of another different genus than to that of the same genus, therefore a revision of the Hamulidae family systematic has been proposed. In the analysis of the U2 snDNA, we were able to corroborate that U2 snDNA and U5 snDNA were linked in the same tandem array, and this has interest for tracing evolutionary lines. The karyotype of the species was composed of 2n = 48 acrocentric chromosomes, and each of the three multigene families were located in different chromosome pairs, thus providing three different chromosomal markers.ConclusionsNovel data can be extracted from the results: a putative event of horizontal transfer, a possible tRNA-derived SINE linked to one of the four 5S rDNA types characterized, and a linkage between U2 and U5 snDNA. In addition, a revision of the taxonomy of the Haemulidae family has been suggested, and three cytogenetic markers have been obtained. Some of these results have not been described before in any other fish species. New clues about the genome organization and evolution of the multigene families are offered in this study.

Highlights

Molecular and cytogenetic markers are of great use for to fish characterization, identification, phylogenetics and evolution
The abnormal structure observed in the other clone of the type δ at the Helix III-Loop C region might be deleterious, since mutations occurring in this region could have lethal effects or affect the translation accuracy [34]; it is possible that the β and δ types of 5S coding region could be pseudogenes
The non-syntenic arrangement of both ribosomal clusters, as we have found in P. mediterraneus, is the most commonly-observed situation in fishes [31]

Summary

Introduction

Molecular and cytogenetic markers are of great use for to fish characterization, identification, phylogenetics and evolution. Multigene families have proven to be good markers for a better understanding of the variability, organization and evolution of fish species. Concerted evolution is the model which has commonly been used to explain the long-term evolution of these multigene families. It has traditionally been thought that nuclear ribosomal DNA (45S and 5S) and U2 small nuclear RNA (snRNA) genes are multigene families that undergo a concerted long-term evolution. At the cytogenetic level the ribosomal RNA genes have been shown to be useful tools for providing chromosome molecular markers [9], for analyzing the evolution processes of species [10] and for phylogenetic analysis and species identification [11]

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