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Genetic characterization of Plectorhinchus mediterraneus yields important clues about genome organization and evolution of multigene families.
Merlo MA
,
Pacchiarini T
,
Portela-Bens S
,
Cross I
,
Manchado M
,
Rebordinos L
.
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BACKGROUND: 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. 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.
RESULTS: Four 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.
CONCLUSIONS: Novel 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.
Figure 1. Secondary structure of the 5S rRNA domain β. 5S rRNA secondary structure from the different types obtained. Only Loop B, Helix III and Loop C are represented. A schematic representation of this region is in the center of the image. The β type did not produce any secondary structure in RNAstructure software. The γ’ type corresponds to the deleted form of this type.
Figure 2. 5S rDNA homology betweenPlectorhinchus mediterraneusandRaja asterias. Schematic representation (left) and alignment (right) in NTS (A) and coding regions (B) of Raja asterias and Plectorhinchus mediterraneus. The boxes in the schematic representation show the aligned region. Rast: Raja asterias; Pmed: Plectorhinchus mediterraneus.
Figure 3. Putative regulatory element inside NTS type α. The 5’ end of the Plectorhinchus mediterraneus NTS type α. The graphic shows the number of species which share the same region in their NTS. The region most shared is highlighted between dotted lines.
Figure 4. tRNA-Gln secondary structure and sequence alignment. Secondary structure (A) and alignment (B) of the tRNA-Gln from a variety organisms of belonging to mammals and fishes. The structures were predicted by RNAstructure 5.2 software, and different temperatures were entered depending on whether the organism is mammal (37°C) or fish (15°C).
Figure 5. U2 snRNA gene structure. Schematic representation of the U2-U5 snDNA cluster (A). The 3’ box and PSE of the U2 snRNA gene (B and E respectively) and of the U5 snRNA gene (C and D respectively), are detected by alignment with other fish sequences (gray boxes). Key: 3’: 3’ box; P1: PSE of U5 snRNA gene; P2: PSE of U2 snRNA gene; Pau: Pagrus auriga; Ppa: Pagrus pagrus; Dsa: Diplodus sargus; Dla: Dicentrarchus labrax; Dpu: Dicentrarchus punctatus; Pme: Plectorhinchus mediterraneus.
Figure 6. Karyotype and Fluorescencein situHybridization inPlectorhinchus mediterraneus. Karyotype of P. mediterraneus composed of 24 acrocentric chromosome pairs (A). Double-FISH treatment to localize simultaneously the 5S rDNA (red) and 18S rRNA genes (green) (B); U2-U5 snRNA gene (red) and 18S rRNA gene (green) (C); and U2-U5 snRNA gene (red) and 5S rDNA (green) (D).
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