Characterization of a complex satellite DNA in the mollusc Donax trunculus: analysis of sequence variations and divergence

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

Background

The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated.

Results

The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies.

Conclusions

This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.

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.

Are Pericentric Inversions Reorganizing Wedge Shell Genomes?

Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10–11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.

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.

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.

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.

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.

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.

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

The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (Protobranchia, Pteriomorphia and Heteroconchia). BIV160 monomers are similar in repeat size and nucleotide sequence to satDNAs described earlier in oysters and in the clam Donax trunculus. The broad distribution of BIV160 satDNA indicates that similar variants existed in the ancestral bivalve species that lived about 540 million years ago; this makes BIV160 the most ancient satDNA described so far. In the species examined, monomer variants are distributed in quite a complex pattern. This pattern includes (i) species characterized by a specific group of variants, (ii) species that share distinct group(s) of variants and (iii) species with both specific and shared types. The evolutionary scenario suggested by these data reconciles sequence uniformity in homogenization-maintained satDNA arrays with the genomic richness of divergent monomer variants formed by diversification of the same ancestral satDNA sequence. Diversified repeats can continue to evolve in a non-concerted manner and behave as independent amplification-contraction units in the framework of a 'library of satDNA variants' representing a permanent source of monomers that can be amplified into novel homogeneous satDNA arrays. On the whole, diversification of satDNA monomers and copy number fluctuations provide a highly dynamic genomic environment able to form and displace satDNA sequence variants rapidly in evolution.

Molecular and cytogenetic characterization of repetitive DNA in the Antarctic polyplacophoran Nuttallochiton mirandus

Two highly repeated DNAs, designated NmE1/NmE2 and NmE5, were identified by EcoRV digestion in the chiton Nuttallochiton mirandus (Mollusca: Polyplacophora). The comparison of the sequences obtained showed high similarity in 5' and 3' regions and the NmE5 sequence displayed an inserted sequence that might arise from a transposable element. Southern blotting analyses suggested a tandem organization of both satellite DNA families identified. Moreover, dot blot analyses, performed on several molluscan species, revealed a different degree of conservation of the repeated DNAs. Fluorescence in-situ hybridizations (FISH) on metaphase chromosomes showed that both satellite DNAs are located at centromeric regions.

Initial analysis of tandemly repetitive sequences in the genome of Zhikong scallop (Chlamys farreri Jones et Preston)

Tandemly repetitive sequences are widespread in all eukaryotic genomes, but data on tandem repeats are limited in Zhikong scallop (Chlamys farreri). In the present study, paired-end sequencing of 2016 individual fosmid clones resulted in 3646 sequences. A total of 2,286,986 bp of genomic sequences were generated, representing approximately 1.84 per thousand of the Zhikong scallop genome. Using tandem repeats finder (TRF) software, a total of 2500 tandem repeats were found, including 313 satellites, 1816 minisatellites and 371 microsatellites. The cumulative length of tandem repeats was 552,558 bp, accounting for 24.16% of total length. Specifically, the length of microsatellites, minisatellites and satellites was 9425, 336,001 and 207,132 bp, accounting for 1.71, 60.81 and 37.49% of the length of tandem repeats, and 0.41, 14.69 and 9.06% of total length, respectively. The detailed information on the characteristic of all repeat units was also represented, which will provide a useful resource for physical mapping and better utilization of the existing genomic information in Zhikong scallop.

Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus)

We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.

Three new satellite sequences and a mobile element found inside HSP70 introns of the Mediterranean mussel (Mytilus galloprovincialis)

We report the characterization of 3 new repetitive sequences from the bivalve mollusc Mytilus galloprovincialis, designated Mg1, Mg2, and Mg3, with monomer lengths of 169, 260, and 70 bp, respectively. The 3 repeats together constitute approximately 7.8% of the M. galloprovincialis genome and were found, together with ApaI-type 2 repeats, inside the introns of 2 genes of the HSP70 family, hsc70 and hsc71. Both the monomer length and the genomic content of the repeats indicate satellite sequences. The Mg1 repetitive region and its flanking sequences exhibit significant homology to CvE, a member of the Pearl family of mobile elements found in the eastern oyster (Crassostrea virginica). Thus, the whole homologous region is designated MgE, the first putative transposable element characterized in M. galloprovincialis. The ApaI, Mg2, and Mg3 repeats are continuously arranged inside the introns of both the hsc70 and hsc71 genes. The presence of perfect inverted repeats flanking the ApaI-Mg2-Mg3 repetitive region, as well as a sequence analysis of the repeats, indicates a transposition-like insertion of this region. The genes of the HSP70 family are highly conserved, and the presence of repetitive DNA or of mobile elements inside their introns is reported here for the first time.

Sequence divergence and conservation in organizationally distinct subfamilies of Donax trunculus satellite DNA

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

Long inversely oriented subunits form a complex monomer of Tribolium brevicornis satellite DNA

Highly abundant satellite DNA named TBREV is detected and characterized in the beetle Tribolium brevicornis (Insecta: Coleoptera). An outstanding peculiarity of the TBREV satellite monomer is its complex structure based on the two approximately 470-bp-long subunits, inversely oriented within a 1061-bp-long monomer sequence. The proposed evolutionary history demonstrates a clear trend toward increased complexity and length of the TBREV satellite monomer. This tendency has been observed on three levels: first as direct and inverted duplications of short sequence motifs, then by inverse duplication of the approximately 470-bp sequence segment, and, finally, by spread of inversely duplicated elements in a higher-order register and formation of extant monomers. Inversely oriented subunits share a similarity of 82% and have a high capacity to form a thermodynamically stable dyad structure that is, to our knowledge, the longest ever described in any satellite monomer. Analysis of divergences between inversely oriented subunits shows a tendency to a further reduction in similarity between them. Except in its centromeric localization, the TBREV satellite does not show similarity to other known Tribolium satellites, either in nucleotide sequence or in monomer length and complexity. However, TBREV shares common features of other Tribolium satellites that might be under functional constraints: nonconstant rate of evolution along the monomer sequence, short inverted repeats in the vicinity of an A+T tract, nonrandom distribution of A or T >/=3 tracts, and CENP-B box-like motifs. Although long inverted subunits might reinforce structural characteristics of the satellite monomer, their nucleotide sequence does not seem to be under constraints in order to preserve the dyad structure.

Preservation and high sequence conservation of satellite DNAs suggest functional constraints

Due to a high evolutionary turnover many satellite DNAs are restricted to a group of closely related species. Here we demonstrate that the satellite DNA family PSUB, abundant in the beetle Palorus subdepressus, is distributed in a low number of copies among diverse taxa of Coleoptera (Insecta), some of them separated for an evolutionary period of up to 60 Myr. Comparison of PSUB cloned from the species Tribolium brevicornis with the PSUB family previously characterized in Palorus subdepressus revealed high sequence conservation and absence of fixed species-specific mutations. The most polymorphic sites are those with ancestral mutations shared among clones of both species. Since the ancestral mutations contribute significantly to overall diversity, it could be proposed that a similar mutational profile already existed in an ancestral species. The pattern of variability along the satellite monomer is characterized by the presence of conserved and variable regions. The nonrandom pattern of variability as well as the absence of sequence divergence is also discerned for PRAT satellite DNA, cloned previously from two Palorus species and a distantly related Pimelia elevata. Since PRAT and PSUB are present in parallel in diverse taxa of Coleoptera, we propose that their long evolutionary preservation suggests a possible functional significance. This indication is additionally supported not only by the high evolutionary conservation of the sequences, but also by the presence of significantly conserved and variable regions along the monomers.

Structure analysis of two Toxoplasma gondii and Neospora caninum satellite DNA families and evolution of their common monomeric sequence

A family of repetitive DNA elements of approximately 350 bp-Sat350-that are members of Toxoplasma gondii satellite DNA was further analyzed. Sequence analysis identified at least three distinct repeat types within this family, called types A, B, and C. B repeats were divided into the subtypes B1 and B2. A search for internal repetitions within this family permitted the identification of conserved regions and the design of PCR primers that amplify almost all these repetitive elements. These primers amplified the expected 350-bp repeats and a novel 680-bp repetitive element (Sat680) related to this family. Two additional tandemly repeated high-order structures corresponding to this satellite DNA family were found by searching the Toxoplasma genome database with these sequences. These studies were confirmed by sequence analysis and identified: (1). an arrangement of AB1CB2 350-bp repeats and (2). an arrangement of two 350-bp-like repeats, resulting in a 680-bp monomer. Sequence comparison and phylogenetic analysis indicated that both high-order structures may have originated from the same ancestral 350-bp repeat. PCR amplification, sequence analysis and Southern blot showed that similar high-order structures were also found in the Toxoplasma-sister taxon Neospora caninum. The Toxoplasma genome database (http://ToxoDB.org ) permitted the assembly of a contig harboring Sat350 elements at one end and a long nonrepetitive DNA sequence flanking this satellite DNA. The region bordering the Sat350 repeats contained two differentially expressed sequence-related regions and interstitial telomeric sequences.

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

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

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.

Cloning and genetic variability of a HindIII repetitive DNA in Acrossocheilus paradoxus (Cyprinidae)

Thirty clones of a highly repetitive HindIII fragment of DNA from seven populations of Acrossocheilus paradoxus (Cyprinidae) were isolated and sequenced. The fragment represents a tandemly repeated sequence, with a monomeric unit of 270 bp, amounting to 0.08-0.10% of the fish genome. Higher units of this monomer appear as a ladder in Southern blots. The HindIII satellite DNA family is conserved in three genera of the Cyprinidae. Variation in nucleotide sequences of this repetitive fragment, which is A+T-rich, is distributed both within individuals and among populations. High overall nucleotide divergence (dij = 0.056 +/- 0.001) was detected among clones of the HindIII satellite DNAs of Acrossocheilus paradoxus. Based on the molecular clock hypothesis, the maximum evolutionary rate was estimated to be 5.3 x 10(-7) substitutions per site per year. Lineage sorting may have contributed to the genetic heterogeneity within individuals and populations. Cladistic analyses indicated a closer phylogeographic relationship between populations of the central and south regions in Taiwan.

Characterization and expression of the mouse endonuclease G gene

Endonuclease G (Endo G) is a nuclease of prokaryotic lineage found in the mitochondria of vertebrates that has been suggested to play a role in mitochondrial DNA (mtDNA) replication. We have isolated and sequenced the entire mouse endo G gene, determined the limits of the mRNA, and mapped the promoter region. The coding sequence of the single copy gene is interrupted by two introns and analysis of the transcripts does not support a model by which more than one Endo G isoform could be produced by alternative splicing. We have also characterized a full-length human Endo G cDNA and comparison at the protein level of the human, bovine, and murine nucleases indicates a high degree of conservation except in the respective mitochondrial targeting signals. Endo G is ubiquitously expressed and the steady-state levels of its mRNA vary by a factor greater than seven between different tissues. The relationship between the mtDNA copy number and Endo G mRNA levels is not strictly proportional but tissues richer in mtDNA have higher amounts of the mRNA and vice versa.