Uniform distribution of satellite DNA variants on the chromosomes of tenebrionid species Alphitobius diaperinus and Tenebrio molitor

Parallelism in evolution of highly repetitive DNAs in sibling species

Characterization of heterochromatin in the flour beetle Tribolium audax revealed two highly repetitive DNA families, named TAUD1 and TAUD2, which together constitute almost 60% of the whole genome. Both families originated from a common ancestral approximately 110-bp repeating unit. Tandem arrangement of these elements in TAUD1 is typical for satellite DNAs, whereas TAUD2 represents a dispersed family based on 1412-bp complex higher-order repeats composed of inversely oriented approximately 110 bp units. Comparison with repetitive DNAs in the sibling species Tribolium madens showed similarities in nucleotide sequence and length of basic repeating units and also revealed structural and organizational parallelism in tandem and dispersed families assembled from these elements. In both Tribolium species, one tandem and one dispersed family build equivalent distribution patterns in the pericentromeric heterochromatin of all chromosomes including supernumeraries. Differences in the nucleotide sequence and in the complexity of higher-order structures between families of the same type suggest a scenario according to which rearranged variants of the corresponding ancestral families were formed and distributed in genomes during or after the speciation event, following the same principles independently in each descendant species. We assume that random effects of sequence dynamics should be constrained by organizational and structural features of repeating units and possible requirements for spatial distribution of particular sequence elements. An interspersed pattern of repetitive families also points to the intensive recombination events in heterochromatin. Synergy between the meiotic bouquet stage and satellite DNA sequence dynamics could make a positive feedback loop that promotes the observed genome-wide distribution. At the same time, considering the abundance of these DNAs in heterochromatin spanning the (peri)centromeric chromosomal segments, we speculate that diverged repetitive sequences might represent the DNA basis of reproductive barrier between the two sibling species.

Higher-order organization and compartmentalization of satellite DNA PIM357 in species of the coleopteran genus Pimelia

The PIM357 satellite DNA family is present in 26 Pimelia taxa (Tenebrionidae, Coleoptera) with endemic congeneric species from the Canary Islands showing higher interrepeat variability than continental ones. In this paper, we compare the repetitive DNA sequences of a Canarian species that has distinct subfamilies of repeat units, P. radula ascendens, with another without such subfamilies, P. sparsa sparsa. The chromosomal localization of the repeat units and the comparison of the variability of randomly cloned monomers to the one estimated by comparing repeat units from dimers and trimers suggest the absence of satellite subfamilies in P. sparsa sparsa. Hence, the repeat units of this species seem to be uniformly and randomly distributed throughout all chromosomes out of one chromosomal pair. On the contrary, P. radula ascendens shows four divergent subfamilies of repeat units supported by several diagnostic nucleotide substitutions. These subfamilies seem to form four distinct repeat units: monomer subfamily 1, monomer subfamily 4 and two higher-order units (dimer linking subfamily 1 and 4, and dimer linking subfamily 2 and 3). Moreover, monomers of subfamily 1 are present in three chromosomal pairs only. We discuss the effect of different potential factors acting in the concerted evolution and the genomic organization of stDNA sequences in these taxa.

Evolutionary dynamics of a satellite DNA in the tiger beetle species pair Cicindela campestris and C. maroccana

Satellite repeat elements are an abundant component of eukaryotic genomes, but not enough is known about their evolutionary dynamics and their involvement in karyotype and species differentiation. We report the nucleotide sequence, chromosomal localization, and evolutionary dynamics of a repetitive DNA element of the tiger beetle species pair Cicindela maroccana and Cicindela campestris. The element was detected after restriction digest of C. maroccana total genomic DNA with EcoRI as a single band and its multimers on agarose gels. Cloning and sequencing of several isolates revealed a consensus sequence of 383 bp with no internal repeat structure and no detectable similarity to any entry in GenBank. Hybridization of the satellite unit to C. maroccana mitotic and meiotic chromosomes revealed the presence of this repetitive DNA in the centromeres of all chromosomes except the Y chromosome, which exhibited only a very weak signal in its short arm. PCR-based tests for this satellite in related species revealed its presence in the sister species C. campestris, but not in other closely related species. Phylogenetic analysis of PCR products revealed well-supported clades that generally separate copies from each species. Because both species exhibit the multiple X chromosome karyotypic system common to Cicindela, but differ in their X chromosome numbers (four in C. maroccana vs. three in C. campestris), structural differences could also be investigated with regard to the position of satellites in a newly arisen X chromosome. We find the satellite in a centromeric position in all X chromosomes of C. maroccana, suggesting that the origin of the additional X chromosome involves multiple karyotypic rearrangements.

DNA characterization and karyotypic evolution in the bee genus Melipona (Hymenoptera, Meliponini)

We analyzed patterns of heterochromatic bands in the Neotropical stingless bee genus Melipona (Hymenoptera, Meliponini). Group I species (Melipona bicolor bicolor, Melipona quadrifasciata, Melipona asilvae, Melipona marginata, Melipona subnitida) were characterized by low heterochromatic content. Group II species (Melipona capixaba, Melipona compressipes, Melipona crinita, Melipona seminigra fuscopilosa e Melipona scutellaris) had high heterochromatic content. All species had 2n = 18 and n = 9. In species of Group I heterochromatin was pericentromeric and located on the short arm of acrocentric chromosomes, while in Group II species heterochromatin was distributed along most of the chromosome length. The most effective sequential staining was quinacrine mustard (QM)/distamycin (DA)/chromomycin A3(CMA3)/4-6-diamidino-2-phenylindole (DAPI). Heterochromatic and euchromatic bands varied extensively within Group I. In Group II species euchromatin was restricted to the chromosome tips and it was uniformly GC+. Patterns of restriction enzymes (EcoRI, DraI, HindIII) showed that heterochromatin was heterogeneous. In all species the first pair of homologues was of unequal size and showed heteromorphism of a GC+ pericentromeric heterochromatin. In M. asilvae (Group I) this pair bore NOR and in M. compressipes (Group II) it hybridized with a rDNA FISH probe. As for Group I species the second pair was AT+ in M. subnitida and neutral for AT and GC in the remaining species of this group. Outgroup comparison indicates that high levels of heterochromatin represent a derived condition within Melipona. The pattern of karyotypic evolution sets Melipona in an isolated position within the Meliponini.

Comparative analysis of different satellite DNAs in four Mytilus species

We report the characterization of three satellite DNAs in four species of mussel: Mytilus edulis, Mytilus galloprovincialis, Mytilus trossulus, and Mytilus californianus. The monomers of the Apa I satellite DNAs were 173, 161, and 166 bp long. These satellite monomers were used to construct phylogenetic trees to infer relationships among these species. The topologies obtained clearly indicate that M. californianus is the most divergent species with respect to the other three. Furthermore, localization of satellite DNAs on metaphase chromosomes was performed using fluorescent in situ hybridization (FISH). Fluorescent signals revealed a different organization and distribution of these three satellite DNAs.

A novel interspersed type of organization of satellite DNAs in Tribolium madens heterochromatin

Analysis of arrangement of satellite DNA sequences in Tribolium madens (Insecta, Coleoptera) by Southern analysis of pulsed-field blots and two colour FISH on extended chromosomes and DNA fibres revealed a novel type of heterochromatin organization. Two satellite DNAs, distributed over the whole pericentromeric heterochromatin of all chromosomes form clusters, ranging in size from 150 kb up to several Mb. Within the clusters, both satellites are in the form of highly interspersed, short homogeneous arrays which vary in size with a lowest length limit of only few kb. The longest arrays composed of a single satellite are relatively short, up to 70 kb for satellite I, and up to 45 kb for satellite II. Only a small fraction of about 15% of satellite II is organized in long tandem repeats, while the rest is in the form of only a few repeats intermingled with satellite I. The results indicate that large clusters composed of interspersed arrays of both satellites represent a major component of T. madens heterochromatin, which is mostly devoid of long regions of other sequences. The same organizational pattern probably also includes a region of the functional centromere. We propose that such an organizational pattern of DNA sequences in heterochromatin might be common in genomes characterized by a high rate of interchromosomal exchange. This pattern of organization is different from that in other animal as well as plant species analysed up to now, in which every satellite in heterochromatin is organized in a small number of large separate domains.

Comparative study of satellite sequences and phylogeny of five species from the genusPalorus(Insecta, Coleoptera)

Major satellite sequences are analysed in the three tenebrionid beetles Palorus cerylonoides, P. genalis, and P. ficicola, and compared with the ones from P. ratzeburgii and P. subdepressus reported elsewhere. All of them are A+T rich, pericentromerically located, and with lengths of about 150 bp, either in the form of monomers or formed by more complex repeating units. A preliminary phylogenetic analysis of Palorus species using the 3' end of the mitochondrial Cytochrome Oxidase I gene shows that the five Palorus species have been diverging for a considerable amount of evolutionary time, with the pair P. ratzeburgii and P. genalis being the most closely related. Only these two taxa showed some similarity between their respective high-copy-number satellite sequences, while other satellites are mutually unrelated and might have originated independently. However, all the satellites have in common tertiary structure induced by intrinsic DNA curvature, a characteristic which is conserved within the genus. Palorus major satellites were previously detected in the genomes of congeneric species as low-copy-number clusters (Meštrovic et al., Mol. Biol. Evol. 15: 1062-1068. 1998). Given the divergences between the analysed species, the substitution rate deduced from high- and low-copy-number repeats is unexpectedly low. The presence of sequence-induced DNA curvature in all Palorus satellites and similar satellite DNAs in the species pair P. ratzeburgii and P. genalis suggest (i) that constraints are at the tertiary structure; and (ii) that the satellite DNA evolutionary turnover can be dependant on the history of the taxa under study, resulting in retention of similar satellites in related taxa.Key words: satellite DNA, evolution, mitochondrial cytochrome oxidase I, DNA curvature.