Satellite DNA-like repeats are dispersed throughout the genome of the Pacific oyster Crassostrea gigas carried by Helentron non-autonomous mobile elements

Abstract

Satellite DNAs (satDNAs) are long arrays of tandem repeats typically located in heterochromatin and span the centromeres of eukaryotic chromosomes. Despite the wealth of knowledge about satDNAs, little is known about a fraction of short, satDNA-like arrays dispersed throughout the genome. Our survey of the Pacific oyster Crassostrea gigas sequenced genome revealed genome assembly replete with satDNA-like tandem repeats. We focused on the most abundant arrays, grouped according to sequence similarity into 13 clusters, and explored their flanking sequences. Structural analysis showed that arrays of all 13 clusters represent central repeats of 11 non-autonomous elements named Cg_HINE, which are classified into the Helentron superfamily of DNA transposons. Each of the described elements is formed by a unique combination of flanking sequences and satDNA-like central repeats, coming from one, exceptionally two clusters in a consecutive order. While some of the detected Cg_HINE elements are related according to sequence similarities in flanking and repetitive modules, others evidently arose in independent events. In addition, some of the Cg_HINE's central repeats are related to the classical C. gigas satDNA, interconnecting mobile elements and satDNAs. Genome-wide distribution of Cg_HINE implies non-autonomous Helentrons as a dynamic system prone to efficiently propagate tandem repeats in the C. gigas genome.

Figure 1

Workflow of the genome-wide identification of tandem repeats and their flanking sequences in the assembled genome of the Pacific oyster Crassostrea gigas.

Figure 2

Correlation between number of monomers, monomer length, and number of arrays. Number of arrays plotted as a function of number of monomers (a), monomer copy number plotted as a function of monomer length (b).

Figure 3

Structural characteristics and sequence comparisons of Cg_HINE elements. Consensus sequences of monomers belonging to each cluster are shown in (a). A general scheme of all depicted CG_HINE elements is presented in the central part of this figure (b). Consensus sequences of left and right flanking sequences (LF and RF, respectively) are presented in (c). Furthermore, elements are grouped according to sequence similarity. Group 1 form Cg_HINEs that share similarity in all element parts. In group 2 there are elements similar in flanking segments but not in monomers building TRs. Group 3 form elements divergent in their nucleotide sequences. Sequence segments corresponding to the structural elements in LF and RF are underlined with the same color as used in schematic presentation in (b). In group 1 monomer consensus sequences (a) boxed are sequence segments with reduced variability compared to monomers from the cluster CL4 (see text for explanation). In all alignments, differences present in less than half of nucleotides at each position are colored.

Figure 4

Schematic presentation of groups of Cg_HINE elements. Related elements of group 1 are shown in (a), related in flanking sequences but with divergent TRs of group 2 are in (b), and divergent in all segments (group 3) are in (c). Shown are also elements with two arrays of TRs, detected in group 1 and 3. Grey tones indicate sequence similarity in flanking segments. Tones of a color in monomers indicate similarity, while different colors indicate unrelated monomer sequences.