Haplotype-specific chromosome painting reveals recombination patterns in a holocentric plant species, preprint reports

A bioRxiv preprint describes the development and application of haplotype-specific oligo-FISH probes for the holocentric sedge species Rhynchospora breviuscula, a member of the beak-sedge genus that comprises approximately 381 species worldwide. Unlike monocentric chromosomes — which have a single, discrete centromere — holocentric chromosomes distribute centromeric activity along virtually the entire chromosome length, creating an unusual context for meiotic recombination.

Using a haplotype-phased genome assembly of Rhynchospora breviuscula (haploid chromosome number n = 5), the research team developed probes targeting chromosomes 1, 2, and 3 that are capable of distinguishing individual homologues. This chromosome-painting approach allowed direct visualisation of recombination events along specific chromosomes in a species where the absence of a single centromeric anchor makes such tracking technically challenging.

The work provides foundational tools for studying how meiotic recombination is organised in holocentric plants — a question with both evolutionary and practical relevance, given that holocentricity is a derived state that has evolved independently multiple times across plants and animals. This is a preprint and has not yet been peer-reviewed.