A single genome is enough: New method SCINKD identifies sex chromosomes with kmer logic
In most vertebrate species, the genetic switch that determines sex is hidden within a small, non-recombining region of the genome—a region that has long resisted complete assembly. Now, a team of evolutionary and computational biologists has developed SCINKD (Sex Chromosome Identification by Negating Kmer Densities), a framework that identifies candidate sex chromosomes from a single diploid individual by detecting diagnostic patterns of sequence divergence between haplotypes. By leveraging whole-genome shotgun sequencing and kmer frequency analysis, the method bypasses the need for comparative genomic data from both sexes or closely related species—traditionally required to distinguish sex chromosomes from autosomes. Applying SCINKD across diverse vertebrate taxa, the authors demonstrate that it can simultaneously pinpoint previously unknown sex chromosome linkage groups and reveal misassembled autosomal regions, offering a powerful tool for population genomics and evolutionary biology.
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