Karyotypic analysis and isolation of four DNA markers of the scleractinian coral Favites pentagona (Esper, 1795) (Scleractinia, Anthozoa, Cnidaria)

We performed conventional and molecular cytogenetic studies on the Favites pentagona Esper, 1795, a scleractinian coral mostly found along the west coast of Japan. Karyotype analysis of F. pentagona by G banding revealed a karyogram containing a homogenously staining region (HSR) on chromosome 10 in more than 50% of the examined metaphase spreads. This HSR consisted of sequences from 18S ribosomal RNA (rRNA) genes, as demonstrated by fluorescence in situ hybridization (FISH) and DNA sequencing. We highlighted the development of four chromosomal FISH markers from repetitive genes such as U2 small nuclear RNA linked to 5S rRNA sequence (U2 snRNA-5S), 18S rRNA, histone H3, and uncharacterized gene FP-9X. The chromosomal locations of the U2 snRNA-5S and 18S RNA were on the terminal end of long arm of chromosomes 2 and 10, respectively, while the histone H3 and the uncharacterized gene were located near the centromeres of chromosomes 1 and 9, respectively. These FISH markers will improve the karyotyping of F. pentagona from mitotic preparations which helps in widening our under-standing of coral genetic structure and chromosome organization. In addition, these improvements in karyotyping will provide the basis in constructing of chromosome-level genome assembly for F. pentagona.

Automated summary

In this study, we conducted karyotype analysis and molecular cytogenetic studies on Favites pentagona, a coral species predominantly found in the western coast of Japan. G banding analysis revealed the presence of a homogenously staining region (HSR) on chromosome 10 in over 50% of examined metaphase spreads. Further investigation through fluorescence in situ hybridization (FISH) and DNA sequencing confirmed that this HSR consisted of sequences derived from 18S ribosomal RNA (rRNA) genes. Additionally, we developed four chromosomal FISH markers from repetitive genes, which will contribute to improved karyotyping and understanding of genetic structure and chromosome organization in F. pentagona. Furthermore, these improvements in karyotyping will serve as a foundation for constructing a chromosome-level genome assembly for this coral species.