Additional file 1 of Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

Additional file 1 : Table S1. The plastome assembly, annotation information, and distributions of genomic rearrangements for the 75 individuals. Table S2. Detailed information of repeat content for the 75 individuals. Repeat content for the three IR regained plastomes were calculated using only one IR copy. Table S3. Repeats mediated tRNA duplicates. For dispersed repeats, F: forward repeat; C: complement repeat; P: palindromic repeat; R: reverse repeat, and the numbers after the colon represent length of dispersed repeats. For tandem repeats, the numbers before the colon represent length of tandem repeats, the content after the colon represent unit size × copy number. Table S4. Repeats around endpoints of inversions. For dispersed repeats, F: forward repeat; C: complement repeat; P: palindromic repeat; R: reverse repeat, and the numbers after the colon represent length of dispersed repeats. For tandem repeats, the numbers before the colon represent length of tandem repeats, the content after the colon represent unit size × copy number. Palindromic repeat (P) are marked in red. Table S5. Palindromic repeat sequences around endpoints of inversions. Table S6. Repetitive DNA in the acquired introns. Table S7. Nucleotide diversity (pi) for different genes, intergenic regions, and datasets. PC, plastid coding regions; PN, plastid noncoding regions; PCN, the whole plastome. Eight highly divergent coding regions (π > 0.04) and 16 highly divergent non-coding regions (π > 0.1) are marked in red. Table S8. Sequence divergence in accD among the IRLC species. Table S9. Sequence divergence in clpP among the IRLC species. Table S10. Sequence divergence in ycf1 among the IRLC species. Table S11. Sequence divergence in matK among the IRLC species. Table S12. Sequence divergence in rbcL among the IRLC species. Table S13. Information of repetitive elements for the coding sequence (CDS) of three genes (accD, clpP and ycf1) with accelerated substitution rates and two relatively conserved genes (matK and rbcL). There is no coding sequence (CDS) in accD for M. polymorpha because it is a pseudogene (truncated sequence). Table S14. Percent repetitive DNA of the three localized hypermutation regions around the three genes (accD, clpP, and ycf1) with accelerated substitution rates and the remaining plastome sequences. Table S15. Locations of the 75 individuals representing 20 Medicago, Trigonella, and Melilotus species. The individuals for which were planted in laboratory are marked by asterisks. Plastomes of Medicago truncatula were assembled from whole-genome resequencing data downloaded from NCBI (SRR1524305 and SRR965443). The outgroup was downloaded from NCBI (NC_011828.1). The individuals for which were chosen as the representatives of each species are marked in red. Table S16. The 73 protein-coding genes (CDS) shared across 21 taxa included in the phylogenetic analysis. Table S17. Taxa included in the synonymous and nonsynonymous divergence analyses of accD, clpP, ycf1, matK, and rbcL. (√) adopt in analysis, (−) not available in NCBI and not adopt in analysis.