Supporting Information Legends
Supporting Figure S1: C. rubella sRNA library quality. Quality was assessed
through size distribution of all reads (A) and unique sequences (B). Additionally, the
first base of each sRNA was examined according to library and read length (C). High
library quality is indicated by the dominant fraction of 21 nt sRNAs having a 5’ uracil
(indicative of miRNAs), and the dominant fraction of 24 nt sRNAs having a 5’
adenosine (indicative of siRNAs).
Supporting Figure S2: miRNA divergence in the Camelineae vs intergenic
regions, transposable elements and genes. (A) Rates of nucleotide substitution in
miRNAs compared with randomly sampled selected genomic features. Box plots
show median values. (B-D) Unpolarized mutation spectrum of miRNA nucleotide
changes compared with other genomic features. p-bootstrap tests, p-values <0.05
for miRNAs lower than genomic features for all deletions/insertions, and p-values
<0.05 for miRNAs higher than the genomic features for G/T, C/T and A/G changes
Supporting Figure S3: Allele frequencies in 80 A. thaliana accessions. To be
included in the dataset, the miRNA sequence had to be covered in at least 80% or
64 of the accessions. Minor allele frequency indicates the number of accessions in
which the least frequently occurring allele was found for (A) miRNAs, (C) miRNA*s,
and miRNA targets (E). Derived allele frequency indicates the number of accessions
in which the non-ancestral allele was found for (B) miRNAs and (D) miRNA*s.
Supporting Figure S4: Geographic distribution of derived miRNA alleles in 80
A. thaliana accessions. Geographic locations of ancestral (red circles), derived
(blue triangles) and minor (white crosses) alleles for selected miRNAs with derived
allele frequencies of ≥ 0.1.
Supporting Figure S5: miRNA polymorphisms in A. thaliana vs. intergenic
regions, transposable elements and genes. (A) Average rate of nucleotide
substitution in miRNAs compared with randomly sampled selected genomic features.
(B-D) Unpolarized mutation spectrum of miRNA nucleotide changes compared with
other genomic features.
Supporting Figure S6: miRNA and target polymorphism spectrum in 80 A.
thaliana accessions.
Supporting Table S1: C. rubella library sequencing depth.
Supporting Table S2: Known syntenic miRNA loci expressed in C. rubella. The
number of detected reads for each miRNA loci is given.
Supporting Table S3: Non-syntenic loci of known miRNAs expressed in C.
rubella. The number of reads, scaffold and position of the mature miRNA is given for
each locus.
Supporting Table S4: miRNA family detection according to algorithm used.
Supporting Table S5: Identification of C. rubella TAS genes by BLAST. Length
and percentage identity of the A. thaliana sequence aligned in the longest match is
given.
Supporting Table S6: Predicted MYB, ARF and PPR/TPR targets of C. rubella
tasiRNAs.
Supporting Table S7: Predicted interspecific miRNA synteny
Supporting Table S8: Interspecific miRNA and miRNA* identification.
Supporting Table S9: Interspecific miRNA differences.
Supporting Table S10: Interspecific miRNA* differences.
Supporting Table S11: Polymorphisms in miRNAs in 80 A. thaliana accessions.
Supporting Table S12: Polymorphisms in miRNA*s in 80 A. thaliana accessions.
Supporting Table S13: Predictions of miRNA* sequences in 80 A. thaliana accessions.