Scientists Map the Chromosomes of a Common Stony Coral, Adding New Tools to Coral Genetics

In a quiet laboratory experiment that began on a summer night off the west coast of Japan, researchers have produced one of the most detailed looks yet at the chromosomes of a stony coral. The species in question, Favites pentagona, a massive or encrusting reef-builder common along Japanese shores, has now become only the sixth scleractinian coral species to receive a full molecular cytogenetic analysis. The work, published in the journal Comparative Cytogenetics, combines classical chromosome staining with modern DNA probe technology to reveal where key genes sit on the coral’s chromosomes, and it uncovers a striking genetic amplification that appears in more than half of the dividing cells examined.

The team collected gamete bundles from spawning colonies at Nishidomari in Kochi Prefecture on the evening of July 24, 2019, when the corals released their eggs and sperm between roughly 8:00 and 9:30 in the evening. After fertilizing the gametes in the laboratory, the researchers treated the embryos with colchicine to arrest cell division at metaphase, the stage at which chromosomes are most condensed and visible. A hypotonic solution spread the chromosomes apart, a methanol-acetic acid fixative preserved them, and the cells were then dropped onto microscope slides where the chromosomes could be stained and examined one by one.

Conventional G-banding, a technique long used in human medical genetics, involves digesting the chromosomes briefly with trypsin and staining them with Giemsa to produce a pattern of light and dark bands. This is notoriously difficult in invertebrates, whose chromosomes are small and respond weakly to the treatment, but the team succeeded in producing readable banding patterns from the coral embryos. Counting across one hundred cells, they determined that Favites pentagona carries a diploid chromosome number of 28, arranged in fourteen pairs. Based on the position of each chromosome’s constriction point, the karyotype consists of six submetacentric and eight metacentric chromosome pairs, ordered from largest to smallest.

The most eye-catching finding came from chromosome 10. In more than fifty percent of the metaphase spreads examined, one copy of this chromosome carried a long, pale-staining stretch known as a homogeneously staining region, or HSR. Such regions arise when a particular stretch of DNA is amplified and repeated many times over within a chromosome, a phenomenon most familiar from tumor cells, where amplified oncogenes can appear as HSRs. Using fluorescence in situ hybridization, or FISH, the researchers showed that this coral HSR is composed of copies of the 18S ribosomal RNA gene, one of the workhorse sequences that cells use to build their protein-making machinery.

FISH works by attaching fluorescently labeled DNA probes to matching sequences on prepared chromosomes, lighting up the exact locations of target genes under a fluorescence microscope. Building on the banding work, the team developed four such probes from tandemly repetitive genes: the 18S ribosomal RNA gene, a fused U2 small nuclear RNA and 5S ribosomal RNA sequence, the histone H3 gene, and an uncharacterized sequence designated FP-9X. Each probe produced a single, bright, unambiguous signal on the chromosomes, even in prometaphase spreads where the chromosomes are elongated and harder to interpret. That specificity is what makes these markers genuinely useful for routine chromosome identification.

The mapping results place each marker at a distinct address. The 18S ribosomal RNA gene cluster sits at the terminal end of the long arm of chromosome 10, coinciding exactly with the HSR. The U2 snRNA-5S marker lights up near the tip of the long arm of chromosome 2. The histone H3 gene maps near the centromere of chromosome 1, and the FP-9X sequence sits at the centromere of chromosome 9. Notably, this is the first time the chromosomal location of a histone H3 locus has been reported in any stony coral, adding a new comparative data point to a very sparse field.

Cloning and sequencing of the probe inserts confirmed their identities and produced some surprises. The 18S ribosomal RNA clone of 1,732 base pairs differed from a known Favites pentagona sequence by just a single nucleotide, and the histone H3 clone matched the known partial sequence exactly. The 824-base-pair U2-5S clone, however, contained not only a 5S ribosomal RNA gene segment but also a complete U2 spliceosomal small nuclear RNA sequence, suggesting that the two genes are fused in this species, likely as a pseudogene. Comparison with sequences from other corals revealed several short insertions unique to the Favites copy, hinting at an interesting evolutionary history for this tandem repeat.

The comparative context is where the study gains its broader significance. Before this report, molecular cytogenetic data existed for only five stony coral species across three families: two Acropora species, two merulinids, and one lobophylliid. The new work brings that tally to six species and adds a second detailed merulinid dataset. Intriguingly, the authors note that homogeneously staining regions have now been found in every non-Acropora species they have examined, appearing on different chromosomes in different species, which suggests that HSRs are a shared cytogenetic characteristic of certain stony coral lineages rather than a one-off anomaly. Meanwhile, the chromosomal position of the conserved histone gene cluster differs between the acroporid and merulinid families, evidence that even highly conserved genomic features have been reshuffled over coral evolution.

Why does this matter beyond the chromosome spread? Stony coral taxonomy is famously difficult. Species boundaries drawn from skeletal morphology often conflict with molecular phylogenies, a problem attributed in part to hybridization between close relatives and to the remarkable morphological plasticity of coral colonies. Cytogenetic characters offer an independent line of evidence that can help untangle these relationships, revealing genome rearrangements, translocations, and duplications that reflect evolutionary history. Reliable chromosome markers also lay the practical groundwork for a chromosome-level genome assembly of Favites pentagona, the kind of high-quality reference genome that anchors modern comparative genomics.

As coral reefs face warming oceans and accelerating decline, understanding coral genome organization is no longer a purely academic pursuit. Chromosome-level tools help researchers compare species, track hybridization, and interpret the genetic basis of traits such as thermal tolerance. With four new FISH markers now validated for Favites pentagona, and a carefully documented karyotype to match genes to chromosomes, this unassuming coral from the coast of Kochi has joined the short list of reef-builders whose genomes can be read at the level of individual chromosomes, one fluorescent signal at a time.

Subject of Research: Karyotyping and chromosomal FISH mapping of the stony coral Favites pentagona

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

Article References: Kawakami, R., Taguchi, T., Vacarizas, J., Ito, M., Mezaki, T., Tominaga, A., & Kubota, S. (2022). Karyotypic analysis and isolation of four DNA markers of the scleractinian coral Favites pentagona (Esper, 1795) (Scleractinia, Anthozoa, Cnidaria). Comparative Cytogenetics, 16(1), 77-92. https://doi.org/10.3897/compcytogen.v16.i1.79953

Image Credits: AI Generated

DOI: 10.3897/compcytogen.v16.i1.79953

Keywords: Favites pentagona, stony corals, cytogenetics, karyotype, FISH, chromosomes, ribosomal RNA, histone H3, genome organization, coral taxonomy, Scleractinia, HSR