Researchers identify oncogene linked to pigmentation patterns in mountain swordtail fish
Researchers have identified the oncogene xmrk as the likely genetic driver behind two distinct melanin-based pigmentation patterns in the mountain swordtail fish Xiphophorus nezahualcoyotl, resolving a debate that has persisted for nearly 100 years. Using a near-complete genome assembly and genome-wide association studies, the team found both the 'spotted side' and 'marmoratus' patterns map to a narrow genomic interval near the sex-determining region. The findings illuminate how complex, repetitive sex chromosome architecture can maintain diverse sex-linked traits and demonstrate the power of long-read sequencing for resolving previously intractable genomic regions.
A new preprint study on bioRxiv reports that two melanin-based pigmentation patterns in the mountain swordtail fish Xiphophorus nezahualcoyotl — known as 'spotted side' and 'marmoratus' — are genetically linked to the oncogene xmrk, located near the sex-determining region of the sex chromosomes. The researchers generated a gapless, near-telomere-to-telomere genome assembly and conducted genome-wide association studies (GWAS) to pinpoint the genomic intervals associated with each pattern. A key finding is that haplotypes containing xmrk can be found on both X and Y chromosomes, and these haplotypes differ dramatically in gene content, structural organization, and accumulation of repetitive elements, including a newly described composite satellite sequence. This structural variability may destabilize the region and influence recombination between haplotypes associated with each pigmentation pattern. The study addresses a longstanding controversy in Xiphophorus biology surrounding the so-called 'macromelanophore determining locus,' which had resisted characterization due to the repetitive and complex nature of sex chromosomes. More broadly, the work highlights how long-read sequencing technologies can unlock phenotypic and evolutionary insights hidden within genomically complex regions. The results have implications for understanding how sex-linked traits diversify across species.
What's missing
As a preprint, this study has not yet undergone peer review, so findings should be interpreted with caution. The study does not fully resolve whether xmrk is the direct causal gene or merely in strong linkage disequilibrium with the true causal variant. Functional validation experiments (e.g., gene knockouts or expression studies) confirming xmrk's mechanistic role in pigmentation are not reported. Additionally, the evolutionary relationship between the oncogenic function of xmrk and its role in normal pigmentation patterning remains an open question.
What different sources said
- bioRxivCenter
Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl
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