Asexual Genome Evolution In The Apomictic Ranunculus auricomus Complex

Asexual lineages are thought to be prone to extinction because of accumulation of deleterious mutations (Muller’s ratchet). Here we analyze genomic effects of hybridity, polyploidy and allelic divergence in apomictic plant lineages, and we identify loci under diversifying selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of 5 genotypes of the Ranunculus auricomus complex, representing 3 sexual and 2 apomictic reproductive biotypes.  The 5 sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent reference assembly of each library separately.  High quality single nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analyzed for signatures of diversifying vs. stabilizing selection. A comparison of polymorphic SNPs between all genotypes supports the hypothesized Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius.  Pairwise comparisons of non-synonymous (dN) to synonymous (dS) substitution ratios between apomictic and sexual genotypes, for  574 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios.  The enrichment analysis of these outliers for gene ontology terms revealed the association of some genes with meiosis and gametogenesis following predictions of diversifying selection between sexual and apomictic genomes. Results suggest that a differential analysis of gene functions is needed to understand effects of mutation accumulation in asexual lineages.