Long-Term Genome Hybridization In Sugarcane Reveals Decoupled Genetic and Epigenetic Effects

Allopolyploidy (interespecific hybridization and polyploidization) induces a myriad of genetic and epigenetic responses, giving rise to new patterns of gene expression, phenotypic variation, chromosomal rearrangements, mobilization of transposable elements, and changes in methylation DNA. We examine the effects of allopolyploidy on repetitive and coding DNA by comparing the genomes of two major sugarcane progenitors (Saccharum officinarum and Saccharum spontaneum) with three derived hybrids (B4362, RB72454 and RB867515). Using Illumina SBS sequencing of genomic DNA we generated over 1 billion of total reads across the five sugarcane genotypes. Analysis of sugarcane coding fraction with sorghum CDS indicates the hybridization in sugarcane sets extensive gene rearrangements - the hybrid RB867515 presented the highest similarity with sorghum comparing to its direct parental RB72454 and S.officinarum. Abundance estimates, based on the reads match to Gramineae repeats, indicate a huge motion of repetitive DNA in hybrids that showed at least double amounts of telomere sequences and loss of ribosomal repeats (1x), comparing with two wild relatives. Since a whole-genome sequence is not available for sugarcane, we used non-cognate assembly for de novo repetitive sequences detection of S.spontaneum and S.officinarum and also performed an assembly of reads that match with sorghum CDS. We were able to identify over 1,400,000 repetitive clusters in both progenitors. Analysis of small RNA sequencing with de novo clusters indicates that most of the small RNAs from sugarcane hybrids are derived from S.officinarum retrotransposons, transposon and MITEs and S.spontaneum coding fraction. These results reflect the decoupled effects of the hybridization on the genetic and epigenetic mechanisms in allopolyploids.