The molecular phylogeny of oysters based on a satellite DNA related to transposons
Introduction
One of the most characteristic features of the eukaryotic genomes is the presence of a variety of repetitive sequences of several types. Among repetitive DNAs, tandemly arranged highly repeated sequences or satellite DNA (Ugarkovic and Plohl, 2002) are the main constituents of the heterochromatin. Thus, different satellite DNA families equilocally accumulate in different regions of the eukaryote chromosomes, mainly at centromeres and in subtelomeric regions (Charlesworth et al., 1994). Several questions remain unresolved concerning the role of these types of sequences within genomes, notably those related to the formation and expansion of a satellite DNA family and its possible function.
Forces governing satellite DNA appearance and amplification are not well understood. An accepted hypothesis suggests the continuous evolution of satellites from pre-existing satellites, through replication slippage and unequal crossing-over mechanisms (Ugarkovic and Plohl, 2002). However, based on recent data, alternative hypotheses are plausible. Thus, new data support the idea that some satellite DNA families originated from retroelements (Batistoni et al., 1995, Kapitonov et al., 1998). Such satellite DNAs could have originated from interspersed retrotansposons by means of unequal crossing-over (Kapitonov et al., 1998), although alternative mechanisms might be operating.
Satellite DNA sequences within genomes, as opposed to the negative view of these sequences as junk DNA, may participate in several cellular processes, as proposed for centromeric DNAs. Centromere-associated satellite DNA could establish a structural context for the action of conserved motifs, such as CENP-B box of α-satellite DNA (Schueler et al., 2001). On the other hand, due to the higher rates of sequence change than in any other parts of the eukaryotic genomes, satellite DNA has been used as a molecular marker for taxonomic and phylogenetic studies (Stepien and Kocher, 1997, Ugarkovic and Plohl, 2002). In particular, among molluscs, comparative studies of satellite DNA sequences have been made in abalone (Muchmore et al., 1998), scallop (Canapa et al., 2000) and mussels (Martínez-Lage et al., 2002).
We have analysed an oyster's satellite DNA family, concluding that it has been derived from a retroelement. Given its presence in several oyster species, we have used it as a marker to clarify several controversial taxonomic aspects. Finally, we have tried to use these sequences as a marker for phylogenetic inference.
Section snippets
Sampling and DNA extraction
We analysed a total of eight oyster species obtained from different locations (Table 1). Genomic DNA from abductor muscle of freshly captured oysters (O. edulis and O. stentina) was purified as in Winnepenninckx et al. (1993). The biological material from C. angulata, C. gigas and C. gasar had been classified by PCR-RFLP of mitochondrial cytochrome oxidase I gene sequence (mtCOI; Boudry et al., 1998, Lapègue et al., 2002). The remaining samples (C. ariakensis, C. sikamea and C. virginica) were
Characterization and conservation of the HindIII satellite DNA
We searched for satellite DNA sequences within the genome of O. edulis by means of genomic-DNA digestions with 20 restriction endonucleases (AluI, BamHI, BclI, BglII, CfoI, DraI, EcoRI, HaeIII, HindII, HindIII, HinfI, HpaII, MspI, NdeII, PstI, PvuII, RsaI, SacI, SspI and XbaI) and subsequent electrophoresis on agarose gels of the generated DNA fragments. Among the different enzymes used, the digestion performed with HindIII, DraI, BclI, HinfI and HaeIII generated a canonical pattern of
Conclusions
In summary, we conclude that:
- (1)
The satellite DNA family that we have studied in oysters, the HindIII family, is conserved in all the species analysed and preserves several molecular specifics common to centromeric satellite DNAs.
- (2)
The presence of the HindIII satellite DNA in the oyster genomes, the homology with satellite DNAs from other bivalves and the homology of all of them with a transposable oyster element appears to indicate the existence of an ancient transposable element, which acted as a
Acknowledgements
This research was supported by two grants from the Plan Andaluz de Investigación (Group No. CVI0200 and Project No. C03-082). We are greatly indebted to Dr. José Ignacio Navas (Centro de Investigación y Formación Acuícola y Pesquera “Agua del Pino”, Huelva, Spain) for his help in sampling and technical assistance.
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