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

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.

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

“…The chromosomal distribution of the most abundant satDNA, CgiSat01, was already described by Wang et al [45] and Tunjić Cvitanić et al [35]. It displayed strong, discrete FISH signals in the centromeric regions of several chromosomes of C. gigas, together with highly interspersed signals on chromosome arms.…”

“…The abundance of satDNAs comprising the satellitome (averaged from the outputs of the four analyses) is relatively low, ranging from 0.01% (which is the bottom cut-off level of the program output) to 0.72% of the genome (Table 1). CgiSat01a and CgiSat01b are variants (sub-families) of the Cg170/HindIII repeat family described by Clabby et al [36] and López-Flores et al [40] and confirmed as the most abundant tandem repeat of this species [35]. A few satDNAs correspond to several clusters of Helitron-incorporated tandem repeats reported by Vojvoda Zeljko et al [37]; in particular, CgiSat01 corresponds to CL1, 2, 10 and 13, CgiSat08 and CgiSat37 to CL 3 and CL 7, respectively, and CgiSat09 to sequences from CL10 and 13.…”

“…A few satDNAs correspond to several clusters of Helitron-incorporated tandem repeats reported by Vojvoda Zeljko et al [37]; in particular, CgiSat01 corresponds to CL1, 2, 10 and 13, CgiSat08 and CgiSat37 to CL 3 and CL 7, respectively, and CgiSat09 to sequences from CL10 and 13. CgiSat17, CgiSat28 and CgiSat46 hold similarity to three clusters of sequences (Cl 112, 460, 150, respectively) enriched in the sample of the immunoprecipitated, CenH3-associated DNA sequences of the Pacific oyster [35].…”

“…For instance, although in C. gigas, the first sequenced bivalve genome, 36% of the assembled sequences were identified as repetitive, 62% of them could not be assigned to any of the known categories. Among those assigned, the majority were characterized as mobile elements, while satDNAs were estimated to make only 1.2% of the genome [35]. Nevertheless, tandem repeats belonging to the most abundant HindIII/Cg170 satDNA, were experimentally estimated to build 1-4% of the genome [36].…”

“…Such a hybrid structure of mobile elements holding tandem repeats could explain the difficulties in both categorizing repetitive sequences in bivalves and determining the precise contribution of each type to the repeatome. For example, after the RepeatExplorer analysis, tandem repeats from central parts of sequences (later recognized as Helitrons) were placed into one cluster and classified as a satellite DNA, while sequences surrounding these central repeats were assigned to other, nonclassified, clusters [35]. In that respect, only more detailed analysis of such sequences could resolve whether they appear in the form of the classical long-array satDNAs, shortarray satDNAs, long-array satDNAs that are associated with mobile elements, short-array satDNAs associated with mobile elements, or in all of the abovementioned forms.…”