Evolutionary turnover of two pBuM satellite DNA subfamilies in the Drosophila buzzatii species cluster (repleta group): From alpha to alpha/beta arrays

Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups

The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology. These studies have been largely concentrated in D. melanogaster and closely related species from the Sophophora subgenus, even though the vast majority of all Drosophila species belong to the Drosophila subgenus. This chapter highlights some studies on the satDNA structure, organization, and evolution in two species groups from the Drosophila subgenus: the repleta and virilis groups. We also discuss and review the classification of other abundant tandem repeats found in these species in the light of the current information available.

Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles

To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.

Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes

Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA) which are among the most abundant, fast evolving (yet poorly studied) genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198) and two novel ones (CDSTR138 and CDSTR130). Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis) and CDSTR198 (in D. buzzatii) in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9-2.9%) within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.

Molecular characterization and chromosomal distribution of a species-specific transcribed centromeric satellite repeat from the olive fruit fly, Bactrocera oleae

Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88%-97%) of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH) of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it's rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages.

The non-regular orbit: three satellite DNAs in Drosophila martensis (buzzatii complex, repleta group) followed three different evolutionary pathways

The genome of species from the buzzatii cluster (buzzatii complex, repleta group) is hosted by a number of satellite DNAs (satDNAs) showing contrasting structural characteristics, genomic organization and evolution, such as pBuM-alpha (~190 bp repeats), pBuM-alpha/beta (~370 bp repeats) and the DBC-150 (~150 bp repeats). In the present study, we aimed to investigate the evolution of these three satDNAs by looking for homologous sequences in the genome of the closest outgroup species: Drosophila martensis (buzzatii complex). After PCR, we isolated and sequenced 9 alpha, 8 alpha/beta and 11 DBC-150 sequences from this species. The results were compared to all pBuM and DBC-150 sequences available in literature. After D. martensis split from the buzzatii cluster some 6 Mya, the three satDNAs evolved differently in the genome of D. martensis by: (1) maintenance of a collection of major types of ancestral repeats in the genome (alpha); (2) fixation for a single major type of ancestral repeats (alpha/beta) or (3) fixation for new divergent species-specific repeat types (DBC-150). Curiously, D. seriema and D. martensis, although belonging to different and allopatric clusters, became independently fixed for the same major type of alpha/beta ancestral repeats, illustrating a rare case of parallelism in satDNA evolution. The contrasting pictures illustrate the diversity of evolutionary pathways a satDNA can follow, defining a "non-regular orbit" with outcomes difficult to predict.

Cactophilic Drosophila in South America: a model for evolutionary studies

The Drosophila buzzatii cluster is composed of seven cactophilic species and their known geographical distribution encompasses the open vegetation diagonal, which includes the morphoclimatic Domains of the Caatinga, Chaco and Cerrado, which are situated between the Amazon and the Atlantic forests. Besides these areas, these cactophilic species are also found in a narrow strip along the Atlantic coast from northeastern Brazil to the southern tip of the country. The hypothesis of vicariant events, defining the core areas of each species, is proposed to explain the historical diversification for the cluster. The intraspecific analysis for the cluster shows a population structure with gene flow restricted by distance, range expansion with secondary contact resulting in introgression and simpatry, especially in the limits of the species distribution, polytypic populations and assortative mating in inter population experiments. There is a variation related to these events that depends on the species and geographic origin of the population analyzed. These events are, hypothetically, described as the results of expansion and retraction of the population ranges, as a consequence of their association with cacti, which theoretically follow the expansion and retraction of dry areas during the paleoclimatic oscillations in South America, as that promoted by the glacial cycles of the Quaternary. The Drosophila buzzatii cluster is divided into two groups. The first one is composed of D. buzzatii, a species that has a broad geographic distribution and no significant differentiation between its populations. The second is the Drosophila serido sibling set, which encompasses the others species and is characterized by a significant potential for differentiation.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

Cellular mechanism for targeting heterochromatin formation in Drosophila

Near the end of their 1990 historical perspective article "60 Years of Mystery," Spradling and Karpen (1990) observe: "Recent progress in understanding variegation at the molecular level has encouraged some workers to conclude that the heterochromatization model is essentially correct and that position-effect variegation can now join the mainstream of molecular biology." In the 18 years since those words were written, heterochromatin and its associated position effects have indeed joined the mainstream of molecular biology. Here, we review the findings that led to our current understanding of heterochromatin formation in Drosophila and the mechanistic insights into heterochromatin structural and functional properties gained through molecular genetics and cytology.

Satellite DNA in insects: a review

The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.

Sequence analysis, chromosomal distribution and long-range organization show that rapid turnover of new and old pBuM satellite DNA repeats leads to different patterns of variation in seven species of the Drosophila buzzatii cluster

We aimed to study patterns of variation and factors influencing the evolutionary dynamics of a satellite DNA, pBuM, in all seven Drosophila species from the buzzatii cluster (repleta group). We analyzed 117 alpha pBuM-1 (monomer length 190 bp) and 119 composite alpha/beta (370 bp) pBuM-2 repeats and determined the chromosome location and long-range organization on DNA fibers of major sequence variants. Such combined methodologies in the study of satDNAs have been used in very few organisms. In most species, concerted evolution is linked to high copy number of pBuM repeats. Species presenting low-abundance and scattered distributed pBuM repeats did not undergo concerted evolution and maintained part of the ancestral inter-repeat variability. The alpha and alpha/beta repeats colocalized in heterochromatic regions and were distributed on multiple chromosomes, with notable differences between species. High-resolution FISH revealed array sizes of a few kilobases to over 0.7 Mb and mutual arrangements of alpha and alpha/beta repeats along the same DNA fibers, but with considerable changes in the amount of each variant across species. From sequence, chromosomal and phylogenetic data, we could infer that homogenization and amplification events involved both new and ancestral pBuM variants. Altogether, the data on the structure and organization of the pBuM satDNA give insights into genome evolution including mechanisms that contribute to concerted evolution and diversification.

Low rates of homogenization of the DBC-150 satellite DNA family restricted to a single pair of microchromosomes in species from the Drosophila buzzatii cluster

A satellite DNA family, termed DBC-150, comprises slightly GC-rich repeat units of approximately 150 bp that were isolated (by DNA digestions or PCR) from the genome of all seven Drosophila species from the buzzatii cluster (repleta group). The presence of subrepeats suggests that part of the extant DBC-150 monomer originated by the duplication of small sequence motifs. The DBC-150 family is compared to the previously described pBuM satDNA family, an abundant component of the genome of five species of the cluster. The two families are different in several aspects, including primary structure, A + T content, intraspecific and interspecific variability and rates of homogenization (or nucleotide spread). The data indicate a lower rate of homogenization (and absence of complete concerted evolution) of the DBC-150 compared to the pBuM family. FISH on metaphase chromosomes revealed that the DBC-150 family is located exclusively in the microchromosomes. To our knowledge this is the first record of a complex Drosophila satDNA restricted to a single pair of microchromosomes. The observed low rates of homogenization of the DBC-150 family might be related to a presumed reduction or suppression of meiotic recombination in the microchromosomes.

Conservation of pBuM-2 satellite DNA sequences among geographically isolated Drosophila gouveai populations from Brazil

In this study, we have compared 34 repetition units of pBuM-2 satellite DNA of individuals from six isolated populations of Drosophila gouveai, a cactophilic member of Drosophila buzzatii cluster (repleta group). In contrast to the results of previous morphological and molecular data, which suggest differentiation among the D. gouveai populations, the sequences and the cluster analysis of pBuM-2 monomers showed that this repetitive element is highly conserved among the six D. gouveai populations (97.8% similarity), indicating a slow rate of evolution of pBuM-2 sequences at the population level. Probably, some homogenization mechanisms of tandem sequences, such as unequal crossing or gene conversion, have maintained the sequence similarity of pBuM-2 among D. gouveai populations. Alternatively, such a result may be associated with a functional role of pBuM-2 sequences, although it is not understood at present.

Aedeagus morphology as a discriminant marker in two closely related cactophilic species of Drosophila (Diptera; Drosophilidae) in South America

Drosophila serido and D. antonietae are sibling species belonging to the Drosophila buzzatii cluster. Morphologically, they can only be discriminated by quantitative traits. In this paper we analyze the length and equalized average curvature of four regions of the aedeagus of D. antonietae and D. serido. Specimens of D. serido and D. antonietae were classified correctly 96.74% of the time. Based only on the variable that most contributed to the discrimination of the groups (equalized average curvature of the arch IV of the aedeagus), we observed significant intraspecific morphological divergence in D. serido in relation to the D. antonietae, in agreement with other markers. The high morphological divergence in equalized average curvature of the arch IV of the aedeagus shows that this region evolved faster than others, since the divergence of the two species. The importance of the present study to the understanding of the genetic basis that controls the formation of the aedeagus, in the species of the Drosophila buzzatii cluster, is discussed.

Repetitive DNA in tropical tasar silkworm Antheraea mylitta

Antheraea mylitta is an endemic insect species producing the world famous tasar silk. Its populations occupying different ecological and geographical regions show certain degree of phenotypic variability for which they are known as 'eco-races'. In order to understand the genetic variability and phylogenetic relationship among the different eco-races we characterized a repetitive TaqI genomic DNA fragment as a genetic marker. The sequence analysis and Southern hybridization show the repetitive nature of TaqI DNA fragment, designated as A. mylitta TaqI family repeat, AmTFR. The PCR amplification of AmTFR reveals its presence in all the tested eco-races of tasar silkworm and some other silk producing insects. The AmTFR is evenly distributed in all 31 meiotic metaphase I chromosomes as observed by fluorescent in situ hybridization. The AmTFR based phylogenetic analysis of the eco-races is not congruent with the morphological variations and their geographical distribution.