Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

Unravelling epigenetic mechanisms in Cerastoderma edule genome: a comparison of healthy and neoplastic cockles

Cancer is a multifaceted genetic disease characterized by the acquisition of several essential hallmarks. Notably, certain cancers exhibit horizontal transmissibility, observed across mammalian species and diverse bivalves, the latter referred to as hemic neoplasia. Within this complex landscape, epigenetic mechanisms such as histone modifications and cytosine methylation emerge as fundamental contributors to the pathogenesis of these transmissible cancers. Our study delves into the epigenetic landscape of Cerastoderma edule, focusing on whole-genome methylation and hydroxymethylation profiles in heathy specimens and transmissible neoplasias by means of Nanopore long-read sequencing. Our results unveiled a global hypomethylation in the neoplastic specimens compared to their healthy counterparts, emphasizing the role of DNA methylation in these tumorigenic processes. Furthermore, we verified that intragenic CpG methylation positively correlated with gene expression, emphasizing its role in modulating transcription in healthy and neoplastic cockles, as also highlighted by some up-methylated oncogenic genes. Hydroxymethylation levels were significantly more elevated in the neoplastic samples, particularly within satellites and complex repeats, likely related to structural functions. Additionally, our analysis also revealed distinct methylation and activity patterns in retrotransposons, providing additional insights into bivalve neoplastic processes. Altogether, these findings contribute to understanding the epigenetic dynamics of bivalve neoplasias and shed light on the roles of DNA methylation and hydroxymethylation in tumorigenesis. Understanding these epigenetic alterations holds promise for advancing our broader understanding of cancer epigenetics.

Dominance of transposable element-related satDNAs results in great complexity of "satDNA library" and invokes the extension towards "repetitive DNA library"

Research on bivalves is fast-growing, including genome-wide analyses and genome sequencing. Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization. Here we characterize the satellitomes of five species in the family Ostreidae (Crassostrea angulata, C. virginica, C. hongkongensis, C. ariakensis, Ostrea edulis), revealing a substantial number of satellite DNAs (satDNAs) per genome (ranging between 33 and 61) and peculiarities in the composition of their satellitomes. Numerous satDNAs were either associated to or derived from transposable elements, displaying a scarcity of transposable element-unrelated satDNAs in these genomes. Due to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs, comparative satellitomics demanded more in-depth analyses than standardly employed. Comparative analyses (including C. gigas, the first bivalve species with a defined satellitome) revealed that 13 satDNAs occur in all six oyster genomes, with Cg170/HindIII satDNA being the most abundant in all of them. Evaluating the "satDNA library model" highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such satellitomes. When repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species, the introduction of the terms "TE library" and "repetitive DNA library" becomes essential.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00218-0.

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

BACKGROUND

Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time.

RESULTS

Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement.

CONCLUSIONS

Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

Investigating the diversification of holocentromeric satellite DNA Tyba in Rhynchospora (Cyperaceae)

BACKGROUND AND AIMS

Satellite DNAs (satDNAs) are repetitive sequences composed by tandemly arranged, often highly homogenized units called monomers. Although satDNAs are usually fast evolving, some satDNA families can be conserved across species separated by several millions of years, probably because of their functional roles in the genomes. Tyba was the first centromere-specific satDNA described for a holocentric organism, until now being characterized for only eight species of the genus Rhynchospora Vahl. (Cyperaceae). Here, we characterized Tyba across a broad sampling of the genus, analysing and comparing its evolutionary patterns with other satDNAs.

METHODS

We characterized the structure and sequence evolution of satDNAs across a robust dadated phylogeny based on Hybrid Target-Capture Sequencing (hyb-seq) of 70 species. We mined the repetitive fraction for Tyba-like satellites to compare its features with other satDNAs and to construct a Tyba-based phylogeny for the genus.

KEY RESULTS

Our results show that Tyba is present in the majority of examined species of the genus, spanning four of the five major clades and maintaining intrafamily pairwise identity of 70.9% over 31 Myr. In comparison, other satellite families presented higher intrafamily pairwise identity but are phylogenetically restricted. Furthermore, Tyba sequences could be divided into 12 variants grouped into three different clade-specific subfamilies, showing evidence of traditional models of satDNA evolution, such as the concerted evolution and library models. Besides, a Tyba-based phylogeny showed high congruence with the hyb-seq topology. Our results show structural indications of a possible relationship of Tyba with nucleosomes, given its high curvature peaks over conserved regions and overall high bendability values compared with other non-centromeric satellites.

CONCLUSIONS

Overall, Tyba shows a remarkable sequence conservation and phylogenetic significance across the genus Rhynchospora, which suggests that functional roles might lead to long-term stability and conservation for satDNAs in the genome.

Satellite DNAs-From Localized to Highly Dispersed Genome Components

According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes' diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome

The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.

Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae)

Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.

Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae)

Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.

The Genomics of Plant Satellite DNA

The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.

First Description of a Satellite DNA in Manatees' Centromeric Regions

Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.

The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs

B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.

A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed

Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BACKGROUND

Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the "repeatome", are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution.

RESULTS

We obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex.

CONCLUSION

This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the "library hypothesis"

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.

Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas

Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons.

The reactivity of hydrazine with photosystem II strongly depends on the redox state of the water oxidizing system

The decay kinetics of the redox states S2 and S3 of the water-oxidizing enzyme have been analyzed in isolated spinach thylakoids in the absence and presence of the exogenous reductant hydrazine. In control samples without NH2NH2 a biphasic decay is observed. The rapid decline of S2 and S3 with YD as reductant exhibits practically the same kinetics with t1/2 = 6-7 s at pH = 7.2 and 7 degrees C. The slow reduction (order of 5-10 min at 7 degrees C) of S2 and S3 with endogenous electron donors other than YD is about twice as fast for S2 as for S3 under these conditions. In contrast, the hydrazine-induced reductive shifts of the formal redox states Si (i = 0...3) are characterized by a totally different kinetic pattern: (a) at 1 mM NH2NH2 and incubation on ice the decay of S2 is estimated to be at least 25 times faster (t1/2 less than or equal to 0.4 min) than the corresponding reaction of S3 (t1/2 approximately 13 min); (b) the NH2NH2-induced decay of S3 is even slower (about twice) than the transformation of S1 into the formal redox state 'S-1' (t1/2 approximately 6 min), which gives rise to the two-digit phase shift of the oxygen-yield pattern induced by a flash train in dark adapted thylakoids. (c) the NH2NH2-induced transformation S0----'S-2' [Renger, Messinger and Hanssum (1990) in: Curr.' Res. Photosynth. (Baltscheffsky, M., ed), Vol. 1, pp. 845-848, Kluwer, Dordrecht] is about three times faster (t1/2 approximately 2 min) than the reaction [see text]. Based on these results, the following dependence on the redox state Si of the reactivity towards NH2NH2 is obtained: S3 less than S1 less than S0 much less than S2. The implications of this surprising order of reactivity are discussed.

A satellite repeat-derived piRNA controls embryonic development of Aedes

Tandem repeat elements such as the diverse class of satellite repeats occupy large parts of eukaryotic chromosomes, mostly at (peri)centromeric and (sub)telomeric regions¹. Some elements, however, are located in euchromatic regions throughout the genome and were hypothesized to regulate gene expression in cis by modulating local chromatin structure, or in trans via repeat-derived transcripts^2–4. Here we show that a satellite repeat in the mosquito Aedes aegypti promotes sequence-specific gene silencing via the expression of two PIWI-interacting RNAs (piRNAs). Whereas satellite repeats and piRNA sequences generally evolve extremely fast^5–7, this locus was conserved for approximately 200 million years, suggesting a central function in mosquito biology. piRNA production commenced shortly after egg-laying, and inactivation of the more abundant of the piRNAs resulted in failure to degrade maternally provided transcripts and developmental arrest. Our results reveal a novel mechanism by which satellite repeats regulate global gene expression in trans via piRNA-mediated gene silencing that is essential for embryonic development.

Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis

Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair

Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.

Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this element.

Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a "DNA remodeling mechanism". The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

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.

Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae

Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes’ centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15–20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.

Natural History of a Satellite DNA Family: From the Ancestral Genome Component to Species-Specific Sequences, Concerted and Non-Concerted Evolution

Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity.

Rex Retroelements and Teleost Genomes: An Overview

Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.

Sex Chromosome Differentiation in the Frog Genus Pseudis Involves Satellite DNA and Chromosome Rearrangements

The genus Pseudis comprises six frogs of the family Hylidae and only P. tocantins had heteromorphic sex chromosomes detected by classical cytogenetics. In this species, the W chromosome is larger than the Z chromosome and has a large heterochromatic block located between the centromere and the nucleolus organizer region (NOR) in the long arm. This large heterochromatic band is enriched for the PcP190 satellite DNA (satDNA), whereas the Z chromosome bears a smaller C-band adjacent to the centromere in the long arm that is not detected by PcP190 probes. To assess sex chromosome differentiation in the genus Pseudis, we investigated the PcP190 satDNA in P. bolbodactyla, P. cardosoi, P. minuta, and P. paradoxa and in one species of Lysapsus, which is the sister genus of Pseudis. PcP190 sequences were isolated, sequenced, and the diversity of this class of satDNA was analyzed. To evaluate whether sex-related variations in PcP190 satDNA were present, we used in situ hybridization (for P. bolbodactyla, P. paradoxa, P. cardosoi, and P. minuta) and Southern blotting analysis (for all species). We found a low level of sex chromosome heteromorphism in P. bolbodactyla, as a PcP190 cluster was detected in the short arm of one of the homologs of pair 7 exclusively in females. In P. paradoxa, P. minuta, and P. cardosoi, PcP190 satDNA is not sex-related, although a cluster of PcP190 sequences could be recognized in the NOR-bearing chromosomes 7 of P. paradoxa and P. minuta and their homologous chromosome 5 of P. cardosoi. By tracking cytogenetic data in a species tree, we may hypothesize that the positioning of the PcP190 site adjacently to the NOR (as observed in the long arm of the W chromosome of P. tocantins) is a derived condition with respect to the location of the PcP190 site apart from the NOR, in the short arm of the NOR-bearing chromosomes 7 (as present in P. bolbodactyla, P. paradoxa, and P. minuta) or 5 (as present in P. cardosoi) and we discuss about the emergence of PcP190 satDNA as a sex-related trait.

New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki

Repetitive DNA represents the major component of the genome in both plant and animal species. It includes transposable elements (TEs), which are dispersed throughout the genome, and satellite DNAs (satDNAs), which are tandemly organized in long arrays. The study of the structure and organization of repetitive DNA contributes to our understanding of genome architecture and the mechanisms leading to its evolution. Molluscs represent one of the largest groups of invertebrates and include organisms with a wide variety of morphologies and lifestyles. To increase our knowledge of bivalves at the genome level, we analysed the Antarctic scallop Adamussium colbecki. The screening of the genomic library evidenced the presence of two novel satDNA elements and the CvA transposon. The interspecific investigation performed in this study demonstrated that one of the two satDNAs isolated in A. colbecki is widespread in polar molluscan species, indicating a possible link between repetitive DNA and abiotic factors. Moreover, the transcriptional activity of CvA and its presence in long-diverged bivalves suggests a possible role for this ancient element in shaping the genome architecture of this clade.

Satellite DNA: An Evolving Topic

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

BACKGROUND

Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.

RESULTS

Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.

CONCLUSIONS

The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.

Methylation profile of a satellite DNA constituting the intercalary G+C-rich heterochromatin of the cut trough shell Spisula subtruncata (Bivalvia, Mactridae)

Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the satellite DNA library hypothesis, we confirmed that this satellite DNA is also present in two other Mactridae species, showing a highly conserved nucleotide sequence together with a dramatic diminution in the number of repeats. Predominantly located at the G + C-rich intercalary heterochromatin of S. subtruncata, SSUsat displays several DNA methylation peculiarities. The level of methylation of SSUsat is high (3.38%) in comparison with bivalve standards and triplicates the mean of the S. subtruncata genome (1.13%). Methylation affects not only the cytosines in CpG dinucleotides but also those in CHH and CHG trinucleotides, a feature common in plants but scarce and without any clear known relevance in animals. SSUsat segments enriched in methylated cytosines partly overlap those showing higher sequence conservation. The presence of a chromosome pair showing an accumulation of markedly under-methylated SSUsat monomers additionally indicates that the methylation processes that shape repetitive genome compartments are quite complex.

Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements

Background

Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape.

Results

We explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences.

Conclusions

The observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3347-1) contains supplementary material, which is available to authorized users.

Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits

Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberolacerta. These families showed different chromosomal locations, abundances, and evolutionary rates. Here, we extend the study of both satellite DNAs (satDNAs) to the remaining Iberolacerta species, with the aim to investigate the patterns of variability and factors influencing the evolution of these repetitive sequences. Our results revealed disparate patterns but also common traits in the evolutionary histories of these satellite families: (i) each satellite DNA is made up of a library of monomer variants or subfamilies shared by related species; (ii) species-specific profiles of satellite repeats are shaped by expansions and/or contractions of different variants from the library; (iii) different turnover rates, even among closely related species, result in great differences in overall sequence homogeneity and in concerted or non-concerted evolution patterns, which may not reflect the phylogenetic relationships among taxa. Contrasting turnover rates are possibly related to genomic constraints such as karyotype architecture and the interspersed organization of diverging repeat variants in satellite arrays. Moreover, rapid changes in copy number, especially in the centromeric HindIII satDNA, may have been associated with chromosomal rearrangements and even contributed to speciation within Iberolacerta.

Structural and functional liaisons between transposable elements and satellite DNAs

Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs exist within a genome. Although they differ in structure, genomic organization, mechanisms of spread, and evolutionary dynamics, TEs and satDNAs can share sequence similarity and organizational patterns, thus indicating that complex mutual relationships can determine their evolution, and ultimately define roles they might have on genome architecture and function. Motivated by accumulating data about sequence elements that incorporate features of both TEs and satDNAs, here we present an overview of their structural and functional liaisons.

High-throughput analysis of the satellitome illuminates satellite DNA evolution

Satellite DNA (satDNA) is a major component yet the great unknown of eukaryote genomes and clearly underrepresented in genome sequencing projects. Here we show the high-throughput analysis of satellite DNA content in the migratory locust by means of the bioinformatic analysis of Illumina reads with the RepeatExplorer and RepeatMasker programs. This unveiled 62 satDNA families and we propose the term "satellitome" for the whole collection of different satDNA families in a genome. The finding that satDNAs were present in many contigs of the migratory locust draft genome indicates that they show many genomic locations invisible by fluorescent in situ hybridization (FISH). The cytological pattern of five satellites showing common descent (belonging to the SF3 superfamily) suggests that non-clustered satDNAs can become into clustered through local amplification at any of the many genomic loci resulting from previous dissemination of short satDNA arrays. The fact that all kinds of satDNA (micro- mini- and satellites) can show the non-clustered and clustered states suggests that all these elements are mostly similar, except for repeat length. Finally, the presence of VNTRs in bacteria, showing similar properties to non-clustered satDNAs in eukaryotes, suggests that this kind of tandem repeats show common properties in all living beings.

Unraveling the Sex Chromosome Heteromorphism of the Paradoxical Frog Pseudis tocantins

The paradoxical frog Pseudis tocantins is the only species in the Hylidae family with known heteromorphic Z and W sex chromosomes. The Z chromosome is metacentric and presents an interstitial nucleolar organizer region (NOR) on the long arm that is adjacent to a pericentromeric heterochromatic band. In contrast, the submetacentric W chromosome carries a pericentromeric NOR on the long arm, which is adjacent to a clearly evident heterochromatic band that is larger than the band found on the Z chromosome and justify the size difference observed between these chromosomes. Here, we provide evidence that the non-centromeric heterochromatic bands in Zq and Wq differ not only in size and location but also in composition, based on comparative genomic hybridization (CGH) and an analysis of the anuran PcP190 satellite DNA. The finding of PcP190 sequences in P. tocantins extends the presence of this satellite DNA, which was previously detected among Leptodactylidae and Hylodidae, suggesting that this family of repetitive DNA is even older than it was formerly considered. Seven groups of PcP190 sequences were recognized in the genome of P. tocantins. PcP190 probes mapped to the heterochromatic band in Wq, and a Southern blot analysis indicated the accumulation of PcP190 in the female genome of P. tocantins, which suggests the involvement of this satellite DNA in the evolution of the sex chromosomes of this species.

RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes

Short interspersed elements (SINEs) are non-autonomous retrotransposons that are widespread in eukaryotic genomes. They exhibit a chimeric sequence structure consisting of a small RNA-related head, an anonymous body and an AT-rich tail. Although their turnover and de novo emergence is rapid, some SINE elements found in distantly related species retain similarity in certain core segments (or highly conserved domains, HCD). We have characterized a new SINE element named RUDI in the bivalve molluscs Ruditapes decussatus and R. philippinarum and found this element to be widely distributed in the genomes of a number of mollusc species. An unexpected structural feature of RUDI is the HCD domain type V, which was first found in non-amniote vertebrate SINEs and in the SINE from one cnidarian species. In addition to the V domain, the overall sequence conservation pattern of RUDI elements resembles that found in ancient AmnSINE (~310 Myr old) and Au SINE (~320 Myr old) families, suggesting that RUDI might be among the most ancient SINE families. Sequence conservation suggests a monophyletic origin of RUDI. Nucleotide variability and phylogenetic analyses suggest long-term vertical inheritance combined with at least one horizontal transfer event as the most parsimonious explanation for the observed taxonomic distribution.

Satellite DNA in Plants: More than Just Rubbish

For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

A novel satellite DNA isolated in Pecten jacobaeus shows high sequence similarity among molluscs

The aim of this work is to investigate the sequence conservation and the evolution of repeated DNA in related species. Satellite DNA is a component of eukaryotic genomes and is made up of tandemly repeated sequences. These sequences are affected by high rates of mutation that lead to the occurrence of species-specific satellite DNAs, which are different in terms of both quantity and quality. In this work, a novel repetitive DNA family, named PjHhaI sat, is described in Pecten jacobaeus. The quantitative analyses revealed a different abundance of this element in the molluscan species investigated in agreement with the "library hypothesis" even if, in this case, at a high taxonomic level. In addition, the qualitative analysis demonstrated an astonishing sequence conservation not only among scallops but also in six other molluscan species belonging to three classes. These findings suggest that the PjHhaI sat may be considered as the most ancients of DNA described so far, which remained "frozen" during molluscan evolution. The widespread distribution of this sat DNA in molluscs as well as its long evolutionary preservation open up questions on the functional role of this element. A future challenge might be the identification of proteins or molecules which interact with the PjHhaI sat.

Novel repeated DNAs in the antarctic polyplacophoran Nuttallochiton mirandus (Thiele, 1906)

Within the scope of a project on the characterization of satellite DNAs in polar mollusks, the Antarctic chiton Nuttallochitonmirandus (Thiele, 1906) was analyzed. Two novel families of tandemly repeated DNAs, namely NmH and NmP, are described in their structure and chromosomal localization, and, furthermore, their presence was analyzed in related species. Data reported here display a particular variability in the structural organization of DNA satellites within this species. Processes driving satellite evolution, which are likely responsible for the intriguing variability of the identified satellite DNAs, are discussed.

Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae)

BACKGROUND AND AIMS

Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size.

METHODS

A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B(6)B(6) (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH).

KEY RESULTS

The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 10(4) to 10(6) copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B(7)B(7) (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers.

CONCLUSIONS

Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B(6)B(6) and B(5)B(5). These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single species. The evolution of the PaB6 copy numbers is discussed, and it is suggested that PaB6 represents a recent and highly dynamic system originating from a small pool of ancestral repeats.

Differential spreading of HinfI satellite DNA variants during radiation in Centaureinae

BACKGROUND AND AIMS

Subtribe Centaureinae appears to be an excellent model group in which to analyse satellite DNA and assess the influence that the biology and/or the evolution of different lineages have had on the evolution of this class of repetitive DNA. Phylogenetic analyses of Centaureinae support two main phases of radiation, leading to two major groups of genera of different ages. Furthermore, different modes of evolution are observed in different lineages, reflected by morphology and DNA sequences.

METHODS

The sequences of 502 repeat units of the HinfI satellite DNA family from 38 species belonging to ten genera of Centaureinae were isolated and compared. A phylogenetic reconstruction was carried out by maximum likelihood and Bayesian inference.

KEY RESULTS

Up to eight different HinfI subfamilies were found, based on the presence of a set of diagnostic positions given by a specific mutation shared by all the sequences of one group. Subfamilies V-VIII were mostly found in older genera (first phase of radiation in the subtribe, late Oligocene-Miocene), although some copies of these types of repeats were also found in some species of the derived genera. Subfamilies I-IV spread mostly in species of the derived clade (second phase of radiation, Pliocene to Pleistocene), although repeats of these subfamilies exist in older species. Phylogenetic trees did not group the repeats by taxonomic affinity, but sequences were grouped by subfamily provenance. Concerted evolution was observed in HinfI subfamilies spread in older genera, whereas no genetic differentiation was found between species, and several subfamilies even coexist within the same species, in recently radiated groups or in groups with a history of recurrent hybridization of lineages.

CONCLUSIONS

The results suggest that the eight HinfI subfamilies were present in the common ancestor of Centaureinae and that each spread differentially in different genera during the two main phases of radiation following the library model of satellite DNA evolution. Additionally, differential speciation pathways gave rise to differential patterns of sequence evolution in different lineages. Thus, the evolutionary history of each group of Centaureinae is reflected in HinfI satellite DNA evolution. The data reinforce the value of satellite DNA sequences as markers of evolutionary processes.

Tandem repeat-containing MITEs in the clam Donax trunculus

Two distinct classes of repetitive sequences, interspersed mobile elements and satellite DNAs, shape eukaryotic genomes and drive their evolution. Short arrays of tandem repeats can also be present within nonautonomous miniature inverted repeat transposable elements (MITEs). In the clam Donax trunculus, we characterized a composite, high copy number MITE, named DTC84. It is composed of a central region built of up to five core repeats linked to a microsatellite segment at one array end and flanked by sequences holding short inverted repeats. The modular composition and the conserved putative target site duplication sequence AA at the element termini are equivalent to the composition of several elements found in the cupped oyster Crassostrea virginica and in some insects. A unique feature of D. trunculus element is ordered array of core repeat variants, distinctive by diagnostic changes. Position of variants in the array is fixed, regardless of alterations in the core repeat copy number. Each repeat harbors a palindrome near the junction with the following unit, being a potential hotspot responsible for array length variations. As a consequence, variations in number of tandem repeats and variations in flanking sequences make every sequenced element unique. Core repeats may be thus considered as individual units within the MITE, with flanking sequences representing a "cassette" for internal repeats. Our results demonstrate that onset and spread of tandem repeats can be more intimately linked to processes of transposition than previously thought and suggest that genomes are shaped by interplays within a complex network of repetitive sequences.

Concerted evolution of satellite DNA in Sarcocapnos: a matter of time

SarkOne is a genus-specific satellite-DNA family, isolated from the genomes of the species of the genus Sarcocapnos. This satellite DNA is composed of repeats with a consensus length of 855 bp and a mean G+C content of 52.5%. We have sequenced a total of 189 SarkOne monomeric repeats belonging to a total of seven species of the genus Sarcocapnos. The comparative analysis of these sequences both at the intraspecific and the interspecific levels have revealed divergence patterns between species are proportional to between-species divergence according to the phylogeny of the genus. Our study demonstrates that the molecular drive leading to the concerted-evolution pattern of this satellite DNA is a time-dependent process by which new mutations are spreading through genomes and populations at a gradual pace. However, time is a limiting factor in the observation of concerted evolution in some pairwise comparisons. Thus, pairwise comparisons of species sharing a recent common ancestor did not reveal nucleotide sites in transitional stages higher than stage III according to the Strachan's model. By contrast, there was a gradation in the percentage of upper transition stages (IV, V, VI) the more phylogenetically distant the species were. In addition, closely related species shared a high number of polymorphic sites, but these types of sites were not common when comparing more distant species. All these data are discussed in the light of current life-cycle models of satellite-DNA evolution.

Analysis of two abundant, highly related satellites in the allotetraploid Nicotiana arentsii using double-strand conformation polymorphism analysis and sequencing

• Allopolyploidy, a driving force in plant evolution, can induce rapid structural changes in parental subgenomes. Here, we examined the fate of homologous subtelomeric satellites in intrasection allotetraploid Nicotiana arentsii formed from N. undulata and N. wigandioides progenitors < 200,000 yr ago. • We cloned and sequenced a number of monomers from progenitors and the allotetraploid. Structural features of both cloned and genomic monomers were studied using double-strand conformation polymorphism analysis. • Two homologous satellites were isolated from N. undulata (called NUNSSP) and N. wigandioides (NWISSP). While the NUNSSP monomers were highly homogeneous in nucleotide sequences, the NWISSP monomers formed two separate clades. Likewise, the genomic NUNSSP monomers showed less DNA conformation heterogeneity than NWISSP monomers, with distinct conformations. While both satellites predominantly occupy subtelomeric positions, a fraction of the NWISSP repeats was found in an intercalary location, supporting the hypothesis that dispersion prevents the repeats becoming homogeneous. Sequence, structural and chromosomal features of the parental satellites were faithfully inherited by N. arentsii. • Our study revealed that intergenomic homogenization of subtelomeric satellite repeats does not occur in N. arentsii allotetraploid. We propose that the sequence and structural divergence of subtelomeric satellites may render allopolyploid chromosomes less vulnerable to intergenomic exchanges.