Table 1. RNA editing sites predicted in Dendrobium nobile chloroplast genome along with its GO annotations.
D. nobile cp genome was BLAST aligned against reference datasets of Nicotiana tabacum, Oryza sativa Japonica Group, Phalaenopsis aphrodite subsp. Formosana, Physcomitrella patens subsp. Patens and Zea mays. Threshold for congruent prediction of RNA editing sites from the reference taxa was set to ≥3 (Count) and 75% (Percentage of prevalence). Count is in the form of (number of reference taxa against which editing site found)/(number of taxa with the homologous site). Further, the genes were exported to OMIX box, blast aligned and subsequently mapped and annotated with Gene ontology (GO) slim terms. Their corresponding GO ids and annotations are shown in the table.
| Gene | GO IDs | GO slim annotation | Nucleotide position | Amino acid position | Triplet position within codon | Base conversion | Codon change | Amino acid conversion | Count | Percentage of Prevalence |
|---|---|---|---|---|---|---|---|---|---|---|
| matK | F: GO:0005198 | F: structural molecule activity | 1258 913 | 420 305 | 1 1 | C→U C→U | CAC→UAC CAU→UAU | H→Y H→Y | 4/5 4/5 | 80 80 |
| P: GO:0006412 | P: translation | |||||||||
| C: GO:0005840; GO:0009507 | C: ribosome; chloroplast | |||||||||
| rps16 | F: GO:0000166; GO:0005215 | F: nucleotide binding; transporter activity | 143 | 48 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| P: GO:0006139; GO:0006810; GO:0009058 | P: nucleobase-containing compound metabolic process; transport; biosynthetic process; | |||||||||
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| atpA | F: GO:0000166; GO:0005215 | F: nucleotide binding; transporter activity | 773 | 258 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 |
| P: GO:0006139; GO:0006810; GO:0009058 | P: nucleobase-containing compound metabolic process; transport; biosynthetic process | |||||||||
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| atpF | F: GO:0005215 | F: transporter activity | 92 | 31 | 2 | C→U | CCA→CUA | P→L | 5/5 | 100 |
| P: GO:0006139; GO:0006810; GO:0009058 | P: nucleobase-containing compound metabolic process; transport; biosynthetic process | |||||||||
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| atpI | F: GO:0005215 | F: transporter activity | 629 | 210 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 |
| P: GO:0006139; GO:0006810; GO:0009058 | P: nucleobase-containing compound metabolic process; transport; biosynthetic process | 428 | 143 | 2 | C→U | CCU→CUU | P→L | 5/5 | 100 | |
| C: GO:0005886; GO:0009507; GO:0009579 | C: plasma membrane; chloroplast; thylakoid | |||||||||
| rpoC1 | F: GO:0003677; GO:0016740 | F: DNA binding; transferase activity | 617 | 206 | 2 | C→U | UCG→UUG | S→L | 5/5 | 100 |
| P: GO:0006139; GO:0009058 | P: nucleobase-containing compound metabolic process; biosynthetic process | 488 | 163 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 | |
| C: GO:0009507 | C: chloroplast | 182 | 61 | 2 | C→U | UCU→UUU | S→F | 5/5 | 100 | |
| 41 | 14 | 2 | C→U | CCA→CUA | P→L | 5/5 | 100 | |||
| rpoB | F: GO:0003677; GO:0016740 | F: DNA binding; transferase activity | 2426 | 809 | 2 | C→U | UCA→UUA | S→L | 4/5 | 80 |
| 623 | 208 | 2 | C→U | CCG→CUG | P→L | 4/5 | 80 | |||
| P: GO:0006139; GO:0009058 | P: nucleobase-containing compound metabolic process; biosynthetic process | 566 | 189 | 2 | C→U | UCG→UUG | S→L | 5/5 | 100 | |
| C: GO:0009507 | C: chloroplast | 551 | 184 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 | |
| 473 | 158 | 2 | C→U | UCG→UUG | S→L | 5/5 | 100 | |||
| 338 | 113 | 2 | C→U | UCU→UUU | S→F | 5/5 | 100 | |||
| rps14 | F: GO:0003723; GO:0005198 | F: RNA binding; structural molecule activity | 149 | 50 | 2 | C→U | CCA→CUA | P→L | 5/5 | 100 |
| P: GO:0006091; GO:0006412; GO:0015979 | P: generation of precursor metabolites and energy; translation; photosynthesis | |||||||||
| C: GO:0009507; GO:0009579; GO:0016020; GO:0005840 | C: chloroplast; thylakoid; membrane; ribosome | |||||||||
| ycf3 | F: GO:0005515 | F: protein binding | 191 | 64 | 2 | C→U | CCA→CUA | P→L | 5/5 | 100 |
| P: GO:0015979 | P: photosynthesis | 185 | 62 | 2 | C→U | ACG→AUG | T→M | 5/5 | 100 | |
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | 44 | 15 | 2 | C→U | UCU→UUU | S→F | 5/5 | 100 | |
| atpB | F: GO:0000166; GO:0005215 | F: nucleotide binding; transporter activity | 1184 | 395 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 |
| P: GO:0006139; GO:0006810; GO:0009058 | P: nucleobase-containing compound metabolic process; transport; biosynthetic process | |||||||||
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| accD | F: GO:0000166; GO:0016740 | F: nucleotide binding; transporter activity | 1184 | 395 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| P: GO:0006139; GO:0006629; GO:0009058 | P: nucleobase-containing compound metabolic process; lipid metabolic process; biosynthetic process | 1412 | 471 | 2 | C→U | CCA→CUA | P→L | 3/3 | 100 | |
| C: GO:0009507 | C: chloroplast | 1430 | 477 | 2 | C→U | CCU→CUU | P→L | 3/3 | 100 | |
| psaI | P: GO:0015979; | P: photosynthesis | 80 | 27 | 2 | C→U | UCU→UUU | S→F | 5/5 | 100 |
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| psbF | F: GO:0003824; GO:0005488 | F: catalytic activity; binding | 77 | 26 | 2 | C→U | UCU→UUU | S→F | 5/5 | 100 |
| P: GO:0006091; GO:0015979; | P: generation of precursor metabolites and energy; photosynthesis | |||||||||
| C: GO:0005739; GO:0009507; GO:0009579; GO:0016020 | C: mitochondrion; chloroplast; thylakoid; membrane | |||||||||
| petL | F: GO:0003824 | F: catalytic activity | 5 | 2 | 2 | C→U | CCU→CUU | P→L | 5/5 | 100 |
| C: GO:0009579 | C: thylakoid | |||||||||
| rpl20 | F: GO:0003723; GO:0005198 | F: RNA binding; structural molecule activity | 308 | 103 | 2 | C→U | UCA→UUA | S→L | 4/5 | 80 |
| P: GO:0006412; GO:0016043 | P: translation; cellular component organization | |||||||||
| C: GO:0005840; GO:0009507 | C: ribosome; chloroplast | |||||||||
| clpP | F: GO:0016787 | F: hydrolase activity | 559 | 187 | 1 | C→U | CAU→UAU | H→Y | 5/5 | 100 |
| P: GO:0019538 | P: protein metabolic process | 82 | 28 | 1 | C→U | CAU→UAU | H→Y | 5/5 | 100 | |
| C: GO:0009507 | C: chloroplast | |||||||||
| petB | F: GO:0003824; GO:0005488 | F: catalytic activity; binding | 611 | 204 | 2 | C→U | UCA→UUA | S→L | 5/5 | 100 |
| P: GO:0006091; GO:0015979 | P: generation of precursor metabolites and energy; photosynthesis | |||||||||
| C:GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | |||||||||
| rpoA | F: GO:0003677; GO:0005515; GO:0016740 | F: DNA binding; protein binding; transferase activity | 830 | 277 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| P: GO:0006139; GO:0009058 | P: nucleobase-containing compound metabolic process; biosynthetic process | 368 | 123 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 | |
| C: GO:0009507 | C: chloroplast | 200 | 67 | 2 | C→U | UCU→UUU | S→F | 3/4 | 75 | |
| rpl2 | F: GO:0003723; GO:0005198; GO:0016740 | F: RNA binding; structural molecule activity; transferase activity | 2 | 1 | 2 | C→U | ACG→AUG | T→M | 5/5 | 100 |
| P: GO:0006412 | P: translation | |||||||||
| C: GO:0005840; GO:0009507 | C: ribosome; chloroplast | |||||||||
| ndhD | F: GO:0003824; GO:0005488 | F: catalytic activity; binding | 878 | 293 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| P: GO:0006091 | P: generation of precursor metabolites and energy | 674 | 225 | 2 | C→U | UCG→UUG | S→L | 4/4 | 100 | |
| C: GO:0009507; GO:0009579; GO:0016020 | C: chloroplast; thylakoid; membrane | 383 | 128 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 | |
| ndhA | F: GO:0003824; GO:0005488 | F: catalytic activity; binding | 473 | 158 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| P: GO:0006091; GO:0015979 | P: generation of precursor metabolites and energy; photosynthesis | |||||||||
| C: GO:0005886; GO:0009507; GO:0009579 | C: plasma membrane; chloroplast; thylakoid | |||||||||
| ndhB | F: GO:0003824; GO:0005488 | F: catalytic activity; binding | 149 | 50 | 2 | C→U | UCA→UUA | S→L | 4/4 | 100 |
| 467 | 156 | 2 | C→U | CCA→CUA | P→L | 4/4 | 100 | |||
| 586 | 196 | 1 | C→U | CAU→UAU | H→Y | 4/4 | 100 | |||
| P: GO:0006091; GO:0015979 | P: generation of precursor metabolites and energy; photosynthesis | 704 | 235 | 2 | C→U | UCC→UUC | S→F | 4/4 | 100 | |
| 737 | 246 | 2 | C→U | CCA→CUA | P→L | 4/4 | 100 | |||
| 830 | 277 | 2 | C→U | UCA→UUA | S→L | 4/5 | 80 | |||
| C: GO:0005886; GO:0009507; GO:0009579 | C: plasma membrane; chloroplast; thylakoid | 836 | 279 | 2 | C→U | UCA→UUA | S→L | 4/5 | 80 | |
| 1481 | 494 | 2 | C→U | CCA→CUA | P→L | 4/4 | 100 | |||
| rpl23 | F: GO:0003723; GO:0005198 | F: RNA binding; structural molecule activity | 71 | 24 | 2 | C→U | UCU→UUU | S→F | 4/5 | 80 |
| P: GO:0006412 | P: translation | |||||||||
| C: GO:0005840; GO:0009507 | C: ribosome; chloroplast |