Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.

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

Scientific Reports ◽

10.1038/s41598-020-71886-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Tanja Vojvoda Zeljko ◽

Martina Pavlek ◽

Nevenka Meštrović ◽

Miroslav Plohl

Keyword(s):

Crassostrea Gigas ◽

Tandem Repeats ◽

Pacific Oyster ◽

Sequence Similarity ◽

Wide Distribution ◽

Mobile Elements ◽

Satellite Dnas ◽

Independent Events ◽

The Pacific ◽

Flanking Sequences

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.

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

Genes ◽

10.3390/genes11060695 ◽

2020 ◽

Vol 11 (6) ◽

pp. 695

Author(s):

Monika Tunjić Cvitanić ◽

Tanja Vojvoda Zeljko ◽

Juan J. Pasantes ◽

Daniel García-Souto ◽

Tena Gržan ◽

...

Keyword(s):

Dna Sequences ◽

Crassostrea Gigas ◽

Pacific Oyster ◽

Repetitive Sequences ◽

Genetic Material ◽

Chromosomal Distribution ◽

Sequence Composition ◽

Specific Distribution ◽

The Pacific ◽

Associated Sequences

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.

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