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

Monika Tunjić-Cvitanić,Miroslav Plohl,Daniel García-Souto,Eva Šatović-Vukšić,Juan J Pasantes,Tonči Cvitanić

doi:10.3390/ijms22136798

Abstract

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.

Highlights

Large fractions of eukaryotic genomes are composed of repetitive DNA sequences that could be either repeated in tandem, among which satellite DNAs dominate, or are interspersed, due to the activity of mobile elements [1,2,3,4,5]
Taking into consideration that a significant part of the C. gigas satellitome shows similarity to Helitron mobile elements (Table 1), we explored what the most common organizational form in which these sequences exist in this genome is: element-associated, standalone or both
The many peculiarities in genome organization already known for C. gigas were furthered in our satellitome analysis

Summary

Introduction

Large fractions of eukaryotic genomes are composed of repetitive DNA sequences that could be either repeated in tandem, among which satellite DNAs (satDNAs) dominate, or are interspersed, due to the activity of mobile elements [1,2,3,4,5]. NGS-related bioinformatics allowed revealing either the complete set of repetitive DNA sequences, the repeatome [8], or the broad collection of satDNAs, the satellitome [9], present in eukaryotic genomes. These approaches showed surprisingly large numbers of satDNAs in eukaryotic genomes, i.e., 62 in the migratory locust Locusta migratoria [9], 129 in the Australian morabine grasshoppers of the genus Vandiemenella [10], 164 in the characiform fish Megaleporinus microcephalus [11] and 37 in the plant Passiflora organensis [12]. The study of the biology of satDNA sequences requires a versatile pool of model systems

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Discussion

Conclusion