Subgenome Fractionation in a Homoploid and Allopolyploid Hybrid Complex

Hybridization and polyploidization are common evolutionary processes in vascular plants. Both processes contribute to the evolution of allopolyploid species, but the unique contributions of hybridization versus polyploidy to these species is not clear. This is partly due to the absence of homoploid hybrid species and allopolyploid species from the same parental diploids. Here, I use a unique species complex in Selaginella to explore the impacts of hybridization and polyploidization on genome evolution. Selaginella is one of the largest genera of lycophytes, despite having one of the smallest nuclear genomes found in vascular plants. The southwestern US and mainland Mexico are a center of functional and taxonomic diversity in Selaginella. Here, in the transition zone between the Lower Colorado River Valley and Arizona Upland subdivisions, diploid hybrids, and allopolyploids of S. arizonica ✕ S. eremophila thrive. Both hybrid taxa have distinct levels of desiccation tolerance and occupy more extreme environments than either of the parents. Using a combination of transcriptome and genome data, I assembled and annotated five reference Selaginella genomes, including the two homoploid and allopolyploid taxa. I investigate the relative contributions of each parent to the genomes of the hybrids and compare the impact of hybridization and polyploidy on genome evolution. A genome content analysis using reciprocal best blast hits (RBH) found strong patterns of biased fractionation in the hybrid complex, each biasing between 12-16% towards one parent. Interestingly, this was a reciprocal pattern, the homoploid and allotetraploid each retained more genomic content from the opposite parent. We determined the maternal origin of the plastid organelles through de novo chloroplast genome assembly, alignment, and phylogenetic inference, which further revealed that more genomic content was retained from the maternal parent. In summary, we believe this is one of the only cases of reciprocal biased fractionation in a hybrid complex