Figure S1. Sequence alignments of the tRNA-related SINE elements found on the nuclear genome of Populus trichocarpa. The region of the tRNA-like sequence is shown by a black line. The poly A rich region is boxed. Regions of A and B box of pol III promoter are shown. The name of the scaffolds where the SINEs were retrieved is written on the left.

Figure S2. Distribution of tRNA genes on B.  distachyon (in red) and A.  thaliana (in blue) chromosomes. Distribution is given per tRNA isoacceptor gene family. Chromosomes are numbered from 1 to 5. The total number (T) of tDNAs per family is given.

Figure S3. Number of tRNA isoacceptors (a) and of tRNA isodecoders (b) per nuclear genome and ratio between the number of tRNA isodecoders and the number of tRNA genes (C) in A.  thaliana (At), M.  truncatula (Mt), P.  trichocarpa (Pt), O.  sativa (Os), B.  distachyon (Bd) and C.  reinhardtii (Cr) nuclear genomes.

Figure S4. Correlation between the number of tRNA gene copies specific for each amino acid and the occurrence frequency of the same amino acid in M.  truncatula, P.  trichocarpa and C.  reinhardtii

Figure S5. Correlation between the number of tRNA gene copies specific for each amino acid and the occurrence frequency of the same amino acid in A.  thaliana. In (a) all amino acids were considered. In (b) the number of tDNA copies corresponding to the amino acids Pro, Ser and Tyr, and present on chromosome 1 were subtracted.

Figure S6. Number of tRNA isodecoders per number of tRNAPhe(GAA) or tRNAGln(CTG) genes in the nuclear genomes of higher plants.

Figure S7. A and B box sequences in A.  thaliana tDNAs. The frequency of each nucleotide is indicated for each position.

Figure S8. tRNAGly-snoRNA co-transcripts in At, Mt and Pt.

Figure S9. tRNAMete-snoRNA co-transcripts in Os and Bd.

Figure S10. Cloverleaf secondary structure of the two orphan tDNAs found in O.  sativa or B.  distachyon. The 50 and 25 bp present upstream and downstream each tDNAs is indicated.

Figure S11. Alignment of pre-tRNATyr and pre-tRNAMete from C.  reinhardtii. One representative of Arabidopsis tRNATyr and one of tRNAMete are also shown. The GCT and GAGT motifs conserved in higher plant tRNAMete are shown in red. The T and G nucleotides conserved between the pre-tRNATyr intronic sequences are indicated by arrows.

Table S1. Accession numbers or websites where tDNAs were retrieved from plant genomes using tRNAscan-SE software.

Table S2. Number of mitochondrial (mt)- or plastidial (pt)-like tDNAs per chromosome.

Table S3. Nuclear tRNA isoacceptor gene content (identified by anticodon) and minimal potential codon recognition pattern (codons) relative to the codon frequency in A.  thaliana and O.  sativa. The codon usage is according to The anticodons are those defined at the DNA level, meaning that the modified bases found at the RNA level and their decoding properties are not described. For example inosine (I) is present at position 34 of tRNAAla(AGC), tRNALeu(AAG), tRNAArg(ACG) or tRNAVal(AAC) or a hypermodified uridine is found at this position in tRNALeu(UAA), (for more details, see For A.  thaliana, all tDNAs were considered.

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