Table 1.
Genes acquired from non-organellar sources prior to the split of red algae and green plants
| Gene name | Putative donor | Localization | Putative functions |
| GCN5-related N-acetyltransferase* | β,γ-Proteobacteria | Cytosol | Arginine biosynthesis |
| Glycyl-tRNA synthetase | Bacteria | Plastid/mitochondria | Translation |
| Dihydrodipicolinate synthase (dapA) | γ-Proteobacteria | Plastid | Lysine biosynthesis |
| ThiC family protein | Bacteria | Plastid | Thiamine biosynthesis |
| 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | Chlamydiae | Plastid | Isoprenoid biosynthesis |
| Polynucleotide phosphorylase | Chlamydiae | Plastid | RNA degradation |
| ATP/ADP translocase† | Chlamydiae | Plastid | ATP/ADP transport |
| MGDG synthase† | Bacteria | Plastid | Lipid biosynthesis |
| Glycerol-3-phosphate acyltransferase† | Chlamydiae | Plastid | Phospholipid biosynthesis |
| Alpha amylase | Chlamydiae | Plastid | Carbohydrate metabolism |
| Sodium:hydrogen antiporter† | Chlamydiae | Plastid | Ion transport |
| 3-Dehydroquinate synthase | β,γ-Proteobacteria | Plastid | Amino acid biosynthesis |
| 2-Methylthioadenine synthetase | Bacteroidetes | Plastid | tRNA modification |
| Uroporphyrinogen-III synthase | Bacteria | Plastid | Porphyrin biosynthesis |
| ACT domain-containing protein† | γ-Proteobacteria | Plastid | Amino acid binding |
| 4-Hydroxy-3-methylbut-2-en-1-yl diphosphate synthase | Chlamydiae | Plastid | Isoprenoid biosynthesis |
| Queuine tRNA-ribosyltransferase | Chlamydiae | Plastid | tRNA modification |
| SAM-dependent methyltransferase† | Bacteria | Cytosol | RNA binding |
| Beta-ketoacyl-ACP synthase (fabF) | Chlamydiae | Plastid | Fatty acid biosynthesis |
| Semialdehyde dehydrogenase | α-Proteobacteria | Cytosol | Amino acid metabolism |
| Diaminopimelate decarboxylase (lysA) | Bacteria | Plastid | Lysine biosynthesis |
| Dihydrodipicolinate reductase (dapB) | Bacteria | Plastid | Lysine biosynthesis |
| Aspartate aminotransferase | Chlamydiae | Plastid | Lysine biosynthesis |
| Leucyl-tRNA synthetase | Bacteria | Plastid/mitochondria | Translation |
| Tyrosyl-tRNA synthetase | Chlamydiae | Plastid/mitochondria | Translation |
| Ribosomal protein L11 methyltransferase | β,γ-Proteobacteria | Cytosol | Amino acid methylation |
| 2-Methylthioadenine synthetase* | Bacteria | Cytosol | tRNA modification |
| GTP binding protein, typA | Chloroflexi | Plastid | Translation elongation |
| Cu-ATPase | Chlamydiae | Plastid | Ion transport |
| 4-Diphosphocytidyl-2-C-methyl-D-erythritol kinase | Chlamydiae | Plastid | Isoprenoid biosynthesis |
| Enoyl-ACP reductase (fabI) | Chlamydiae | Plastid | Fatty acid biosynthesis |
| Histidinol-phosphate transaminase | Chloroflexi | Plastid | Histidine biosynthesis |
| Florfenicol resistance protein* | δ-Proteobacteria | Cytosol | Fe-S-cluster binding |
| 23S rRNA (Uracil-5-)-methyltransferase | Chlamydiae | Plastid | RNA modification |
| Topoisomerase 6 subunit B† | Crenarchaea | Cytosol | Protein binding |
| tRNA methyltransferase | Bacteria | Plastid/cytosol | RNA processing |
| Isoleucyl-tRNA synthetase | Bacteria | Cytosol | Translation |
*Genes for which plastid-derived homologs already exist in plants. †Genes that likely possessed novel functions and whose homologs are rarely found in cyanobacteria. For all other genes, the possibility of them resulting from displacement of an endogenous homolog cannot be excluded. The putative donors of these genes are determined without invoking secondary HGT events. Alternative explanations for each gene are discussed in the text and Additional data file 1.