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Abstract: Satellite DNAs (tandemly repeated, non-coding DNA sequences) stretch over almost all native centromeres and surrounding pericentromeric heterochromatin. Once considered as inert by-products of genome dynamics in heterochromatic regions, recent studies showed that satellite DNA evolution is interplay of stochastic events and selective pressure. This points to a functional significance of satellite sequences, which in (peri)centromeres may play some fundamental functional roles. First, specific interactions with DNA-binding proteins are proposed to complement sequence-independent epigenetic processes. The second role is achieved through RNAi mechanism, in which transcripts of satellite sequences initialize heterochromatin formation. In addition, satellite DNAs in (peri)centromeric regions affect chromosomal dynamics and genome plasticity. Paradoxically, while centromeric function is conserved through eukaryotes, the profile of satellite DNAs in this region is almost always species-specific. We argue that tandem repeats may be advantageous forms of DNA sequences in (peri)centromeres due to concerted evolution, which maintains high intra-array and intrapopulation sequence homogeneity of satellite arrays, while allowing rapid changes in nucleotide sequence and/or composition of satellite repeats. This feature may be crucial for long-term stability of DNA-protein interactions in centromeric regions. [Copyright &y& Elsevier]

Abstract: Two related satellite DNA families (satellite I and satellite II) with complex higher-order repeat (HOR) monomers represent major DNA components equilocated in the pericentromeric heterochromatin of all Tribolium madens chromosomes. Fragments obtained upon genomic DNA restriction revealed two subfamilies of satellite II monomers, and also identified regions of transition between satellite I and satellite II sequences. The two subfamilies differ not only in diagnostic nucleotides, but also in flipped orientation of constituent subunits. Hybrid genomic fragments comprise directly linked satellite I and satellite II monomers that cannot be distinguished from randomly cloned monomers of corresponding families. An exception is the most proximal satellite I monomer in the hybrid fragment named TMADhinf, which shows sequence divergence typical for repeats evolving at array ends, in zones of low homogenization efficiency. This pattern points to the extensive rearrangement processes generating abrupt transitions between satellite arrays combined with array maintenance by unequal crossover. Switching points between adjacent satellites as well as the edges of flipped subunits are localized within a short sequence segment, indicating a preferential site of recombination within satellite subunits. Multiple copies of TMADhinf junction fragment support the hypothesis that sites of evolutionary origin of novel satellite repeat (sub)families can be localized at array ends, in regions of enhanced sequence divergence. [Copyright &y& Elsevier]

Abstract: Characterization of a low-copy number DTF1 satellite DNA detected in the bivalve mollusk Donax trunculus revealed extensive grouping of monomer sequence variants into subfamilies identified by distinctive combinations of diagnostic nucleotides. It can be anticipated that a large number of subfamilies exists in the genome. In addition to the tandem organization of 169 bp long monomers, at least one subfamily was created through amplification of adjacent repeats in a higher order register. This complex satellite unit consists of two distinctive monomer variants that differ both in specific nucleotide changes and in a deleted segment partially substituted with a short unrelated sequence element. Most of the nucleotide substitutions differing between subfamilies are highly homogenized within a corresponding group of monomer variants, and intra-subfamily variability in general is low. Nucleotide diversity analysis of all sequenced variants of DTF1 satellite revealed the presence of two conserved segments, while the rest of the monomer sequence shows uniform and considerably higher level of variability. The persistence of conserved segments stands in contrast to the sequence and organizational divergence of monomer variant groups, and may indicate constraints in the evolution of DTF1 satellite repeats. [Copyright &y& Elsevier]

Two satellite DNAs, TANAPH and TDEST, isolated from the beetle species Tribolium anaphe and Tribolium destructor, respectively, are characterized and compared with previously described Tribolium satellites, in order to deduce possible constraints on satellite sequence evolution between closely related species. Sequence diversity analysis of cloned monomers reveals the presence of variable and conserved segments in both satellites. In addition, non-random organization of As or Ts and their periodical distribution in the form of A or T ≥3 tracts, as well as CENP-B box-like motifs and dyad structures have been found in both satellites. Similar structural features are also present in satellites from other Tribolium species. We therefore propose that they, together with the observed non-constant rate of evolution along the satellite sequence, could be related to putative protein binding sites and suggest a possible selective pressure affecting these sequences. Tribolium satellites, including TANAPH and TDEST, are located in the pericentromeric heterochromatin of all chromosomes of the corresponding species. Since satellites from different species exhibit no significant sequence homology, we propose that they did not originate from a common ancestral sequence. More probably, they derive from simple sequence modules some of which could represent protein binding sites. Shuffling of simple sequence modules could generate different satellites, able to perform a similar role in different species. [Copyright &y& Elsevier]

Abstract: Sequence variability and distribution of a newly characterized MPA2 satellite DNA family are described in five root-knot nematode species of the genus Meloidogyne, the mitotic parthenogens M. paranaensis, M. incognita, M. arenaria and M. javanica, and the meiotic/mitotic M. hapla (isolates A and B, respectively). The lack of distinctive mutations and the considerable contribution (40.8%) of ancestral changes disclose an ancient satellite DNA which existed in the common ancestor of extant parthenogenetic species in the same or similar form and remained preserved for a period of at least 43 My. Nonuniformly distributed polymorphic sites along the satellite monomer suggest differences in constraints acting on particular sequence segments. Sequence diversity is clearly unaffected by significant differences in genomic abundance of the MPA2 satellite DNA in the examined species. Observed results suggest that the dynamics of this satellite DNA family might be in the first instance a consequence of characteristics of its nucleotide sequence and possible constraints imposed on it. Under conditions of mitotic and meiotic parthenogenesis, slow accumulation of mutations and slow replacement of old MPA2 sequence variants with new ones may be equivalent to the dynamics of some satellite DNA sequences conserved for extremely long evolutionary periods in sexual species. [Copyright &y& Elsevier]

Abstract: Two satellite DNAs have been characterized in the mitotic parthenogenetic root-knot nematodes Meloidogyne javanica and M. paranaensis, agriculturally important phytoparasitic species. The satellite repeat variants cloned from M. javanica could not be resolved from those described earlier in M. arenaria [Castagnone-Sereno, P., Leroy, F., Abad, P., 2000. Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria. Genome 43, 346–353] and are therefore classified as a single satellite named MARJA. However, this satellite shows 34.3% sequence divergence in comparison with the MPA1 satellite characterized in M. paranaensis, and monomer variants of both satellites are clearly distinguished by homogenized nucleotide substitutions. Nucleotide variability analysis revealed in one segment of the satellite monomer domains of high and low variability, conserved both within and between monomer variants of the two satellites. Intersatellite conservation of these domains indicates evolution of satellite sequence under different constraints, probably due to some functional interactions. In addition, high intrasatellite homogeneity, presence of ancestral mutations in groups of MARJA monomers in both M. javanica and M. arenaria and highly homogenized divergent positions in comparison with the MPA1 indicate similar sequence dynamics in mitotic parthenogenetic taxa to that observed in amphimictic species. [Copyright &y& Elsevier]

Satellite DNA sequence evolution has been studied in several insect species from the genus Pimelia (Tenebrionidae, Coleoptera). Low-copy number homologs of the previously characterized major satellite DNA from P. monticola (PMON) have been cloned and sequenced from six congeneric species belonging to two species groups: Ibero-Balearic and Moroccan. Sequence analysis of a sample of low-copy number repeats revealed two subfamilies, differing on average 17.5% due to randomly spread single point mutations. Each subfamily is specific for a group of taxa in congruence with their biogeography. Within each group, there is no significant species-specific clustering of the sequences. These results suggest that the two satellite subfamilies arose after the split of an ancestral lineage into the North African and Ibero-Balearic Pimelia species-groups, but before their subsequent radiation. Rate heterogeneity tests suggest that PMON sequences have evolved faster in the lineage leading to the Moroccan group. Comparison of sequence divergences between minor PMON and the previously characterized major PIM357 satellite obtained from the same taxa, points to similar evolutionary dynamics. Both sequences are evolving in parallel accumulating mutations in a gradual manner irrespectively of significant differences in abundance. These data show that copy number of the sequence families does not necessarily affect the sequence change dynamics of satellite repeats. [Copyright &y& Elsevier]