Abstract
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.
Highlights
Bivalve mollusks play important roles in marine and freshwater ecosystems throughout the world, in biofiltration, bioremediation, nutrient cycling and storage, stimulation of primary and secondary production, in creation and modification of habitats, biogeochemical transformations, and environmental monitoring
Sequence clustering resulted in 83,856 clusters, and those constituting ≥ 0.01% of the genome were classified by the RepeatExplorer pipeline (Table 1)
Repeat content of C. gigas genome was accessed via RepeatExplorer clustering (Table 1)
Summary
Bivalve mollusks play important roles in marine and freshwater ecosystems throughout the world, in biofiltration, bioremediation, nutrient cycling and storage, stimulation of primary and secondary production, in creation and modification of habitats, biogeochemical transformations, and environmental monitoring. Their importance is highlighted when invasive bivalve species invade new ecosystems where they can achieve very high abundance, causing significant effects on the food webs [1]. Their large commercial importance is reflected by a million-ton production of these organisms, as they represent a food source around the world [1].
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