Organization of Long Repeats of Sex-Chromosomal Heterochromatin in Common Vole Species

Two long repeats, MS3 and MS4, are predominantly located in sex-chromosomal heterochromatin in common vole species [1]. Their tandem arrangement was revealed by means of the PCR analysis of genomic DNAs of four Microtus species and by restriction mapping of clones selected from a M. rossiaemeridionalis genomic library. Several mobile elements proved to be incorporated in a monomeric unit of each repeat and amplified together with its other components. In addition, LINE inserts were found in MS4 tandem arrays. The copy number of both repeats per haploid genome was estimated at 100–300 for euchromatin and 20,000–40,000 for the M. rossiaemeridionalis genome. The repeats were assumed to be the major component of sex-chromosomal heterochromatin DNA.     

Genomic organization and chromosomal localization of a new repeat MS7, specific for heterochromatin of sex chromosomes in Microtus species voles of the arvalis group

The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis [1, 2]. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M. arvalis. It has been shown by analyzing the phage genomic clones that one MS4 copy makes a part of a monomeric unit exceeding 8.5 kb that also includes a new MS7 repeat and, possibly, LINE fragments. MS7 is located together with MS4 in heterochromatin of common vole sex chromosomes, but in a substantially lesser amount. Probably, as a result of an evolutionary transition of an original repeat from euchromatin of the X chromosome to heterochromatin of the Y chromosome, MS4 underwent multiple amplification, and MS7 spread throughout heterochromatin, being surrounded by the MS4 tandem arrays.     

A Novel MS7 Repeat Specific for Heterochromatin of Sex Chromosomes in Voles of Genus Microtus, Group arvalis: Genomic Organization and Chromosomal Localization

The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M. arvalis. It has been shown by analyzing the phage genomic clones that one MS4 copy makes a part of a monomeric unit exceeding 8.5 kb that also includes a new MS7 repeat and, possibly, LINE fragments. MS7 is located together with MS4 in heterochromatin of common vole sex chromosomes, but in a substantially lesser amount. Probably, as a result of an evolutionary transition of an original repeat from euchromatin of the X chromosome to heterochromatin of the Y chromosome, MS4 underwent multiple amplification, and MS7 spread throughout heterochromatin, being surrounded by the MS4 tandem arrays.     

Detection of tandem repeats in the genome of Citellus genus using restrictases

DNA from ground squirrels of the Citellus genus (Rodentia, Sciuridae) were analysed by centrifugation in the presence of CsCl followed by digestion by restriction endonucleases. Digestion of DNA of two species C. undulatus and C. fulvus by 10 of the 16 restriction endonucleases used led to formation of electrophoretically discrete fragments that are multiple to 330 b.p. in length which points out the tandem organization of repetitive sequences similar to the satellite DNA of many mammal species. However, upon centrifugation we failed to reveal a satellite band in these species; hence the tandem repeats refer to the class of cryptic satellites in the ground squirrels and do not differ in base composition from the remaining part of DNA. The main fraction of the genome was revealed in the form of discrete fragments by cleavage with HindIII and AluI. Both of these restriction endonucleases were used for comparative analysis of DNA of 12 Citellus species. It has been shown that DNA of all species can be digested by HindIII and yields a series of fragments that are multiple to 330-30 b.p. in length and the total content of which varies from species to species within 4-22%. The fraction of the tandem repeats does not correlate with the systematic position of species nor with the amount of heterochromatin in the chromosomes. AluI cuts the DNA of 11 species yielding 110 and 220 b.p. fragments compared to only 60 and 280 b.p. in the DNA of C. dauricus. Under HindIII digestion we can also reveal the tandem repeats in marmot, which is phylogenetically close to the Citellus of the Marmota genus, but they have another periodicity--180 b.p. We propose that the age of ground squirrels repeats is 2-3 million years and they are significantly younger than the marmot repeats.     

The heterochromatin regions of the mitotic chromosomes in cattle]

Cytochemical and molecular peculiarities of heterochromatic regions of bovine chromosomes have been studied, using specific fluorochrome staining induced decondensation, in situ hybridization, pretreatment of restriction enzymes. The heterochromatin of autosomes demonstrated a strong homogeneity. In chromosome Y two small specific heterochromatic regions were found lacking a long repeated tandem block of nucleotides enriched in GC base pairs and having no tandem block of Bkm repeats (10(4) b.p.). This class repeats are probably interspersed in the bovine genome. A rather seldom character of mammalian karyotypes is the absence of cytochemical heterochromatin in the X chromosome.     

Satellite repeats in the functional centromere and pericentromeric heterochromatin of <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Most eukaryotic centromeres contain long arrays of tandem repeats, with unit lengths of 150–300 bp. We searched for such repeats in the functional centromeres of the model legume Medicago truncatula (Medicago) accession Jemalong A17. To this end three repeats, MtR1, MtR2 and MtR3, were identified in 20 Mb of a low-pass, whole genome sequencing data set generated by a random shotgun approach. The nucleotide sequence composition, genomic organization and abundance of these repeats were characterized. Fluorescent in situ hybridization of these repeats on chromosomes at meiosis I showed that only the MtR3 repeat, encompassing stretches of 450 kb to more than 1.0 Mb, is located in the functional portion of all eight centromeres. MtR1 and MtR2 occupy distinct regions in pericentromeric heterochromatin. We also studied the presence and distribution of MtRs in Medicago accession R108-1, a genotype with a genome that is 20% smaller than that of Jemalong A17. We determined that while MtR3 is also centromeric on all pachytene bivalents in R108-1, MtR1 and MtR2 are not present in the R108 genome.     

The 1.688 repetitive DNA of Drosophila: concerted evolution at different genomic scales and association with genes

Concerted evolution leading to homogenization of tandemly repeated DNA arrays is widespread and important for genome evolution. We investigated the range and nature of the process at chromosomal and array levels using the 1.688 tandem repeats of Drosophila melanogaster where large arrays are present in the heterochromatin of chromosomes 2, 3, and X, and short arrays are found in the euchromatin of the same chromosomes. Analysis of 326 euchromatic and heterochromatic repeats from 52 arrays showed that the homogenization of 1.688 repeats occurred differentially for distinct genomic regions, from euchromatin to heterochromatin and from local arrays to chromosomes. We further found that most euchromatic arrays are either close to, or are within introns of, genes. The short size of euchromatic arrays (one to five repeats) could be selectively constrained by their role as gene regulators, a situation similar to the so-called "tuning knobs."     

Molecular cloning and characterization of novel centromeric repetitive DNA sequences in the blue-breasted quail (Coturnix chinensis,Galliformes)

A new family of centromeric highly repetitive DNA sequences was isolated from EcoRI-digested genomic DNA of the blue-breasted quail (Coturnix chinensis, Galliformes), and characterized by filter hybridization and chromosome in situ hybridization. The repeated elements were divided into two types by nucleotide length and chromosomal distribution; the 578-bp element predominantly localized to microchromosomes and the 1,524-bp element localized to chromosomes 1 and 2. The 578-bp element represented tandem arrays and did not hybridize to genomic DNAs of other Galliformes species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and guinea fowl (Numida meleagris). On the other hand, the 1,524-bp element was not organized in tandem arrays, and did hybridize to the genomic DNAs of three other Galliformes species, suggesting that the 1,524-bp element is highly conserved in the Galliformes. The 578-bp element was composed of basic 20-bp internal repeats, and the consensus nucleotide sequence of the internal repeats had homologies to the 41-42 bp CNM repeat and the XHOI family repeat of chicken. Our data suggest that the microchromosome-specific highly repetitive sequences of the blue-breasted quail and chicken were derived from a common ancestral sequence, and that they are one of the major and essential components of chromosomal heterochromatin in Galliformes species.     

Rapid divergence of repetitive DNAs in Brassica relatives

Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid divergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have diverged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed divergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid Brassica genomes; however, this sequence was not identified in the related species. In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability. These results provide insight into genome evolution during polyploidization in Brassica and divergence within the Brassicaceae.     

TRbase: a database relating tandem repeats to disease genes for the human genome

MOTIVATION: Tandem repeats are associated with disease genes, play an important role in evolution and are important in genomic organization and function. Although much research has been done on short perfect patterns of repeats, there has been less focus on imperfect repeats. Thus, there is an acute need for a tandem repeats database that provides reliable and up to date information on both perfect and imperfect tandem repeats in the human genome and relates these to disease genes. RESULTS: This paper presents a web-accessible relational tandem repeats database that relates tandem repeats to gene locations and disease genes of the human genome. In contrast to other available databases, this database identifies both perfect and imperfect repeats of 1-2000 bp unit lengths. The utility of this database has been illustrated by analysing these repeats for their distribution and frequencies across chromosomes and genomic locations and between protein-coding and non-coding regions. The applicability of this database to identify diseases associated with previously uncharacterized tandem repeats is demonstrated.     

Remarkable sequence signatures in archaeal genomes

Complete archaeal genomes were probed for the presence of long (> or = 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.     

Quantitative investigation of reproduction of condensed chromatin of sex chromosomes during trophoblast cell polyploidization and endoreduplication in the East European field vole Microtus rossiaemeridionalis

Simultaneous measurement of DNA content in cell nuclei and condensed chromatin bodies formed by heterochromatized regions of sex chromosomes (gonosomal chromatin bodies, GCB) has been performed in two trophoblast cell populations of the East-european field vole Microtus rossiaemeridionalis, namely in the proliferative population of trophoblast cells of the junctional zone of placenta and in the secondary giant trophoblast cells. One or two gonosomal chromatin bodies have been observed in trophoblast cell nuclei of all embryos studied (perhaps both male and female), In the proliferative trophoblast cell population, characterized by low ploidy levels (2c-16c), and in the highly polyploid population of secondary giant trophoblast cells (16c-256c), the total DNA content in GCB increased proportionally to the ploidy level. In separate bodies, the DNA content rose also in direct proportion with the ploidy level seen in the nuclei with both one and two GCBs in the two trophoblast cell populations. A certain increase in percentage of the nuclei with 2-3 GCBs was shown in the nuclei of the junctional zone of placenta; this may be accounted for by genome multiplication via uncompleted mitoses. In the secondary giant trophoblast cell nuclei (16c-256c), the number of GCBs did not exceed 2, and the share of nuclei with two GCBs did not increase, thus suggesting the polytene nature of sex chromosome in these cells. At different poloidy levels, the ratio of DNA content in the nucleus to the total DNA content in GCB did not change significantly giving evidence of a regular replication of sex chromosomes in each cycle of genome reproduction. In all classes of ploidy, the mean total DNA content in trophoblast cell nuclei with single heterochromatic body was less than in the nuclei with two and more GCBs. This may indicate that a single GCB in many cases does not derive from the fusion of two GCBs. To put it another way, in the nuclei with one GCB and in those with two or more GCBs, different chromosome regions may undergo heterochromatization. The regularities observed here are, most probably, associated with the peculiarities in the structure of X- and Y-chromosomes in a range of species of Microtus (M. agrestis, M. rossiaemeridionalis, M. transcaspicus). As a result, gonosomal chromatin bodies may include large blocks of both constitutive heterochromatin of X- and Y-chromosomes (in male and female embryos) and inactivated euchromatin of "lyonized" X-chromosome in female embryos. Therefore the presence of two or more GCBs in trophoblast cells of M. rossiaemeridionalis may be accounted for by both polyploidy and functional state of the nucleus, in which gonosomal constitutive heterochromatin and inactivated euchromatin form two large chromocenters rather than one. The differences in DNA content in GCBs in the nuclei with one and two GCBs seem to be an indirect indication that the two chromocenters may be formed by two different gonosomes, with the extent of their heterochromatization being higher than that in the nuclei with one GCB. GCBs in the trophoblast cells of M. rossiaemeridionalis are observed not only at the early developmental stages, as it was observed in rat at the first half of pregnancy (Zybina and Mosjan, 1967), but also at the later stages, up to the 17th day of gestation. At these stages, the nuclei with non-classical polytene chromosomes rearrange to those with a great number of endochromosomes, probably because of disintegration of chromosomes into oligotene fibrils. However, it does not seem unlikely that this process may involve heterochromatized gonosomal bodies, since only one or two large GCBs can be seen in the nuclei as before. The presence of prominent blocks of constitutive heterochromatin seems to favor a closer association of sister chromatids in polytene chromosomes, which prevents their dissociation into endochromosomes with the result that polyteny of sex chromosomes in the field vole trophoblast is probably retained during a longer period of embryonic development.     

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.     

Assessing the role of tandem repeats in shaping the genomic architecture of great apes

Background

Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal.

Methodology and Principal Findings

Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements.

Significance

Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.     

The extensive amplification of heterochromatin in Melipona bees revealed by high throughput genomic and chromosomal analysis

Satellite DNAs (satDNAs) and transposable elements (TEs) are among the main components of constitutive heterochromatin (c-heterochromatin) and are related to their functionality, dynamics, and evolution. A peculiar case regarding the quantity and distribution of c-heterochromatin is observed in the genus of bees, Melipona, with species having a low amount of heterochromatin and species with high amount occupying almost all chromosomes. By combining low-pass genome sequencing and chromosomal analysis, we characterized the satDNAs and TEs of Melipona quadrifasciata (low c-heterochromatin) and Melipona scutellaris (high low c-heterochromatin) to understand c-heterochromatin composition and evolution. We identified 15 satDNA families and 20 TEs for both species. Significant variations in the repeat landscapes were observed between the species. In M. quadrifasciata, the repetitive fraction corresponded to only 3.78% of the genome library studied, whereas in M. scutellaris, it represented 54.95%. Massive quantitative and qualitative changes contributed to the differential amplification of c-heterochromatin, mainly due to the amplification of exclusive repetitions in M. scutellaris, as the satDNA MscuSat01-195 and the TE LTR/Gypsy_1 that represent 38.20 and 14.4% of its genome, respectively. The amplification of these two repeats is evident at the chromosomal level, with observation of their occurrence on most c-heterochromatin. Moreover, we detected repeats shared between species, revealing that they experienced mainly quantitative variations and varied in the organization on chromosomes and evolutionary patterns. Together, our data allow the discussion of patterns of evolution of repetitive DNAs and c-heterochromatin that occurred in a short period of time, after separation of the Michmelia and Melipona subgenera.

     

Human Microsatellites: Mutation and Evolution

Microsatellites (MSs) are short tandem DNA repeats with the repetitive motif of two to six nucleotides, forming tracts up to hundreds of nucleotides long. Notwithstanding the active use of MSs in genetic studies of various biological problems, the reasons for their wide occurrence in the genome, their possible functions, and mutational behavior are still unclear. The mutation rate in MS repeats is on average several orders of magnitude higher than in the remaining DNA, which allows for direct estimation of evolutionary transformation rate in nucleotide sequences of the genome. Mutation process in MSs is highly heterogeneous, with distinct differences between species; furthermore, within a species it differs among loci with different repeat size, among alleles of one locus, and among individuals of different sex and age. Most MS mutations are caused by DNA slippage during replication but the probability of this event depends on the locus. In this review, a number of models of MS evolution are discussed, which account for the relationship between mutation rate and allele size, different mutation direction in alleles of different size, and the appearance of point mutations within repeat tracts restricting allele size. The MS evolution is considered mainly in the context of selective neutrality, although there is evidence showing functional significance of some variants of tandem repeats and thus their possible selective value.     

EcoRI- and BamHI-families of repeated sequences in mustelids

The restriction enzymes EcoRI and BamHI digest the genomic DNAs from six mustelids species Mustela lutreola, M. vision, M. erminea, M. sibirica, Vormela peregusna, producing repeated fragments varying in length. Some fragments were hybridized to chromosomes and restriction digests of DNAs from some mustelids and other mammals. The 0.7 kb EcoRI repeats from DNA of M. erminea are dispersed over chromosomes of carnivors. The 1.35, 1.9 and 2.7 kb BamHI repeats from DNA of polecat M. putorius furo are specific for mustelids. These repeats demonstrate interspecific variation in length and the number of copies. All BamHI repeats have no strict tandem organization. The 1.9 kb BamHI repeats are concentrated in the heterochromatic pericentromeric regions and additional chromosome arms. The 1.35 kb BamHI repeats are only located in the centromeric regions of chromosomes of five species and are absent in Vormela peregusna.     

Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

Background and Aims

The genus Fritillaria (Liliaceae) comprises species with extremely large genomes (1C = 30 000–127 000 Mb) and a bicontinental distribution. Most North American species (subgenus Liliorhiza) differ from Eurasian Fritillaria species by their distinct phylogenetic position and increased amounts of heterochromatin. This study examined the contribution of major repetitive elements to the genome obesity found in Fritillaria and identified repeats contributing to the heterochromatin arrays in Liliorhiza species.

Methods

Two Fritillaria species of similar genome size were selected for detailed analysis, one from each phylogeographical clade: F. affinis (1C = 45·6 pg, North America) and F. imperialis (1C = 43·0 pg, Eurasia). Fosmid libraries were constructed from their genomic DNAs and used for identification, sequence characterization, quantification and chromosome localization of clones containing highly repeated sequences.

Key Results and Conclusions

Repeats corresponding to 6·7 and 4·7 % of the F. affinis and F. imperialis genome, respectively, were identified. Chromoviruses and the Tat lineage of Ty3/gypsy group long terminal repeat retrotransposons were identified as the predominant components of the highly repeated fractions in the F. affinis and F. imperialis genomes, respectively. In addition, a heterogeneous, extremely AT-rich satellite repeat was isolated from F. affinis. The FriSAT1 repeat localized in heterochromatic bands makes up approx. 26 % of the F. affinis genome and substantial genomic fractions in several other Liliorhiza species. However, no evidence of a relationship between heterochromatin content and genome size variation was observed. Also, this study was unable to reveal any predominant repeats which tracked the increasing/decreasing trends of genome size evolution in Fritillaria. Instead, the giant Fritillaria genomes seem to be composed of many diversified families of transposable elements. We hypothesize that the genome obesity may be partly determined by the failure of removal mechanisms to counterbalance effectively the retrotransposon amplification.     

Lineage-Specific Tandem Repeats Riding on a Transposable Element of MITE in <Emphasis Type="Italic">Xenopus</Emphasis> Evolution: A New Mechanism for Creating Simple Sequence Repeats

Xstir is a repetitive DNA sequence element that is extremely amplified as a common component of two different structures: a tandem repeat (Xstir array) and a MITE (miniature inverted-repeat transposable element) in the genome of Xenopus laevis. To elucidate the origin and evolutionary history of Xstir-related sequences, we investigated their species specificity among three Xenopus species (X. laevis, X. borealis, and X. tropicalis). Analyses by sequence alignment and digestion with restriction enzymes of genomic Xstir-related sequences revealed that the MITE (Xmix MITE) was well conserved among the three Xenopus species, with small lineage-specific differences. On the other hand, the tandem repeat element (tropXstir) in X. tropicalis was different from the Xstir that X. laevis and X. borealis have in common. Both sequences of Xstir and tropXstir were, however, different segments of the Xmix MITE. The results suggest that these tandem repeats were formed by partial tandem duplication of the MITE internal sequence in each lineage of X. tropicalis and of X. borealis/X. laevis after their branching. A molecular mechanism for creating and elongating the tandem repeats from the MITE is proposed.Reviewing Editor: Dr. Jerzy Jurka     

From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carterae

Dinoflagellate genomes present unique challenges including large size, modified DNA bases, lack of nucleosomes, and condensed chromosomes. EST sequencing has shown that many genes are found as many slightly different variants implying that many copies are present in the genome. As a preliminary survey of the genome our goal was to obtain genomic sequences for 47 genes from the dinoflagellate Amphidinium carterae. A PCR approach was used to avoid problems with large insert libraries. One primer set was oriented inward to amplify the genomic complement of the cDNA and a second primer set would amplify outward between tandem repeats of the same gene. Each gene was also tested for a spliced leader using cDNA as template. Almost all (14/15) of the highly expressed genes (i.e. those with high representation in the cDNA pool) were shown to be in tandem arrays with short intergenic spacers, and most were trans-spliced. Only two moderately expressed genes were found in tandem arrays. A polyadenylation signal was found in genomic copies containing the sequence AAAAG/C at the exact polyadenylation site and was conserved between species. Four genes were found to have a high intron density (>5 introns) while most either lacked introns, or had only one to three. Actin was selected for deeper sequencing of both genomic and cDNA copies. Two clusters of actin copies were found, separated from each other by many non-coding features such as intron size and sequence. One intron-rich gene was selected for genomic walking using inverse PCR, and was not shown to be in a tandem repeat. The first glimpse of dinoflagellate genome indicates two general categories of genes in dinoflagellates, a highly expressed tandem repeat class and an intron rich less expressed class. This combination of features appears to be unique among eukaryotes.