Association Of Intron Loss With Mutation Rate In Arabidopsis Thaliana And A. Lyrata

Intron losses are common during the evolution of eukaryotes. The selective forces acting onthem, however, have not been extensively explored. After the divergence from Arabidopsislyrata10million years ago, Arabidopsis thaliana lost about half of its genome and experiencedan elevated rate of intron loss. It is suggested that the selective force acting on genome reductionalso has driven intron losses. However, the selective force acting on genome reduction is still indebate.To acquire more intron losses than a previous study, we included more outgroup species andconstructed nucleotide alignments, instead of protein alignments. Orthologs that do not presentin synteny blocks between species were filtered in order to exclude paralogs from orthologs. Theannotations of introns involved in intron losses and intron gains were verified by transcriptomedata. The cases that were not supported by transcriptome data were filtered out. The evidence forreverse transcriptase-mediated intron loss is not found from the intron loss dataset. Thenonhomologous end-joining repair of double-strand breaks might be the dominant mechanism ofintron loss in A. thaliana and A. lyrata. Neither of the models could explain the higher rate ofintron loss in A. thaliana than A. lyrata at the mutational level.Intron-lost genes were found to have significantly higher synonymous substitution rates. Byanalyzing the synonymous substitution rates between closely related species, it is found that thehigher substitution rates couldn’t be explained by the abandon of splicing signal or theindel-associated substitution. The differences in mutability among different introns are conservedamong Arabidopsis and closely related species, therefore, the nucleotide substitution rates oforthologous introns in closely related species could represent the mutation rates of Arabidopsisintrons, either lost or extant. As a result, the mutation rates of lost introns are significantlyhigher than extant introns. The analyses of two common kinds of regulatory elements, CpGislands and intron-mediated enhancement signals, suggest that the difference between lost intronsand extant introns could not be explained by regulatory elements. Comparing to A. lyrata atgenome-wide level, A. thaliana has a higher mutation rate, which correlates with the higher rateof intron loss and rapid genome reduction in A. thaliana. Mutation rate is significantly negatively correlated with intron number and intron density. The results indicate that selection to minimizemutational hazards might be the selective force acting on intron loss, and possibly also forgenome reduction, in the evolution of A. thaliana.Small genome size and lower genome-wide intron density are considered to correlate withphenotypic features, such as high metabolic rates and rapid growth. By suggesting that selectionfor rapid growth might indirectly increase mutational hazards, we suggested that themutational-hazard hypothesis is compatible with these correlations.