The molecular phylogeny of oysters based on a satellite DNA related to transposons

Abstract

We have analysed a centromeric satellite DNA family that is conserved in several commercial and non-commercial oyster species (Ostrea edulis, O. stentina, Crassostrea angulata, C. gigas, C. gasar, C. ariakensis, C. virginica and C. sikamea). This satellite DNA family is composed of AT-rich repeat sequences of 166±2 bp and presents a 9-bp motif similar to the mammalian CENP-B box. The homology of oyster HindIII satellite DNA with satellite DNAs from other bivalves and its relation to a part of a mobile element suggest the existence of an ancient transposable element as a generating unit of satellite DNA in bivalve molluscs. Taking advantage of its degree of conservation in oyster species, we have used this element as a taxonomic marker. This marker clearly supports a high degree of differentiation between O. edulis and O. stentina, and, conversely, upholds the contention that C. gigas and C. angulata are the same species. Finally, we have used HindIII satellite DNA as a phylogenetic marker between these species, revealing two clades, one formed by Asiatic species (C. angulata, C. gigas and C. ariakensis) and another by the European, American and African species (O. edulis, C. virginica and C. gasar, respectively).

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.