New method traces ancestry of hybrids binghamtonu NatureComms
= 13 provides a balance between k-mers that are too short or too long . Given an annotation of transposable element content of a genome, it is a simple matter to identify those TE families that overlap subgenome-specific k-mers.
Operationally we begin with chromosomes grouped into homoeologous pairs, triples, quartets, etc. as appropriate for tetraploid, hexaploid, octoploid, etc. genomes. We then identify k-mers that have high copy number across the entire polyploid genome , scan each homoeologous group to identify high copy k-mers that are enriched in one homoeolog vs.
We organize chromosomes into subgenomes by hierarchical clustering based on their shared content of potentially subgenome-enriched high copy k-mers, usingclusters correspond to chromosome sets of shared ancestry. If a progenitor experienced a species-specific expansion of repetitive elements, then we expect to find a corresponding set of k-mer markers enriched in the subgenome descended from that progenitor, relative to one or more of the others.
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