Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in some scallops (Bivalvia: Pectinidae)

Abstract

This study was designed to characterize the 5S ribosomal DNA repeat unit and to evaluate its phylogenetic informativeness in Mimachlamys varia, Hinnites distortus, Aequipecten opercularis and Pecten maximus, scallops of the bivalve family Pectinidae. The repeat unit was PCR amplified and several products cloned and sequenced. The deduced coding region covered 120 bp, showed 52-53% GC content and an identifiable internal promoter. The spacer region was 313-345 bp in length with 30-40% GC and the ends contained elements showing similarity with upstream and downstream sequences involved in the transcription. The sequences of P. maximus were identical and those of M. varia and H. distortus differed only at 2-3 positions. However, the sequences of A. opercularis showed a percentage of differences of 0.69-9.15%, distinguishing two types of units differing in sequence and length of the spacer region. All scallops displayed an identical gene sequence, except M. varia that differed by one nucleotide substitution, but a highly variable spacer. In the phylogenetic trees the sequences grouped by species with two well supported clades, one containing the sequences of M. varia and H. distortus and the other those of P. maximus and A. opercularis, the latter grouped according to the unit type. The topology obtained was in accordance with scallop evolutionary relationships inferred from previous phylogenetic studies.

Long-Term Evolution of 5S Ribosomal DNA Seems to Be Driven by Birth-and-Death Processes and Selection in Ensis Razor Shells (Mollusca: Bivalvia)

“…The presence of several 5S rDNA variants has been reported in other bivalve molluscs, such as Mytilus mussels (Insua et al 2001), the scallop Aequipecten opercularis (López-Piñón et al 2008), and the cockle Cerastoderma glaucum (Freire et al 2005), and in echinoderms (Caradonna et al 2007), arthropods (Keller et al 2006), and chordates (Martins and Galetti 2001;Daniels and Delany 2003). In other examples, 5S rDNA was found to be homogenized within the genome (Brown and Sugimoto 1974).…”

“…In several animal phyla, however, examples have been reported in which sequence divergence levels between ribosomal genes or spacers seem to be much higher than expected under a strict concerted evolution scenario (e.g., Insua et al 2001;Leo and Barker 2002;Freire et al 2005;Keller et al 2006;Sword et al 2007;Caradonna et al 2007;López-Piñón et al 2008).…”

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

“…However, the presence of several 5S rDNA variants has been reported in such diverse taxa as molluscs [8,12,13,67], echinoderms [68] and arthropods [10]. Among fishes, highly variable paralogs have been clearly documented in the 5S rDNA regions in species of the Leporinus genus [25], in the Nile tilapia Oreochromis niloticus [42], in Merlucius species [28], distinct Actinopterygii fish orders [9,24] and in marine Elasmobranchii [29,30].…”

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

“…Even though the 5S rRNA gene is highly conserved, even among unrelated species, the NTS are variable both in length and sequence. These discrepancies have been used as molecular phylogenetic and species-specific markers in several bivalve mollusc species [ 24 , 26 , 55 , 72 ], so that the 5S rDNA is a good candidate to identify molecular markers suitable for distinguish related species.…”

“…But bivalve molluscs stand out for being one of the most extensively studied group of organisms regarding 5S rDNA and ITS region, showing high levels of gene organization as well as a vast diversity of gene arrangements. Molecular organization of ITS region and 5S rDNA has been studied in cockles [ 26 – 28 , 43 ], mussels [ 44 ], oysters [ 9 , 10 ], scallops [ 41 , 42 , 45 , 46 , 55 ], razor clams [ 25 , 99 , 100 ] and Veneroida clams [ 3 ], but it have never been studied in the wedge clams of the genus Donax .…”