Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation

Abstract

Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here, we analyse genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of five genotypes of the Ranunculus auricomus complex, representing three sexual and two apomictic reproductive biotypes. The five sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. 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 analysed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of nonsynonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.

Living on the edge: Conservation genetics of seven thermophilous plant species in a High Arctic archipelago

“…The risk of inbreeding depression may for instance be low for Botrychium lunaria as this is a pteridophyte that reproduces by intragametophytic self-fertilization and is expected to have undergone purging of deleterious recessive alleles (Farrar 2006). Similarly, Ranunculus wilanderi is apomictic and will not experience any increase in homozygosity with decreasing population size (Richards 2003; Pellino et al 2013). Furthermore, like many other pteridophytes, the subterranean, gametophytic phase of B. lunaria is also highly dependent on its mycorrhizal fungal partner (Farrar 2006; Winther and Friedman 2007).…”

Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis

“…The longest putative ORF from any particular sequences were selected. When two similarly long (within 90% of each other) ORFs were found located in opposite strands of the contigs, we followed the method of Pellino [51] by comparing the polarity of the ORFs with the strand orientation from the Blastx analysis. A custom Perl script was used to test whether these SNPs resulted in an amino acid change in the predicted ORF.…”

Diplosporous development in Boehmeria tricuspis: Insights from de novo transcriptome assembly and comprehensive expression profiling

“…Recently, NGS has been employed to investigate changes in gene transcript abundance in apomicts relative to sexual individuals4142, which has provided evidence for differential transcriptional pathways between them and enhanced our understanding of the complexity of gene expression, regulation, and networks in apomictic species. In the present study, we used the Illumina sequencing platform to focus on transcriptome differences between the global gene expression patterns of sexual and apomictic flowers over four developmental stages.…”