Table 5.
Genes Selected as Phylogenetic Correlates Specific to Each Tree Branch
| DI score | Syn prot | Gene | Profile | Protein function | |
|---|---|---|---|---|---|
| Branch CyaPar | |||||
| 1 | 0.0400 | sll0534 | clpP | 10001000000000000000 | ATP-dep. translocation rel. protease |
| 2 | 0.0400 | slr0739 | crtE | 10001000000000000000 | geranylgeranyl pyrophosphate synthase |
| 3 | 0.0400 | slr2075 | groES | 10001000000000000000 | 10kD chaperonin 1 |
| 4 | 0.0400 | slr1808 | hemA | 10001000000000000000 | transfer RNA-Gln reductase |
| 5 | 0.0400 | sll1599 | mntA | 10001000000000000000 | Mn transporter |
| 6 | 0.0400 | sll1600 | mntB | 10001000000000000000 | Mn transporter |
| 7 | 0.0400 | sll0622 | nadA | 10001000000000000000 | quinolinate synthetase |
| 8 | 0.0400 | slr2034 | ycf | 10001000000000000000 | hypothetical protein |
| 9 | 0.0400 | slr2073 | ycf | 10001000000000000000 | hypothetical protein |
| 10 | 0.0400 | slr0181 | ycf | 10001000000000000000 | hypothetical protein |
| 11 | 0.0400 | slr1552 | ycf | 10001000000000000000 | hypothetical protein |
| 12 | 0.0400 | sll1702 | ycf | 10001000000000000000 | hypothetical protein |
| Branch Nongreen algae (and CyaPar) | |||||
| 1 | 0.1192 | sll1325 | atpD | 10011001000010001000 | ATP synthase d subunit |
| 2 | 0.1192 | sll1323 | atpG | 10011001000010001000 | ATP synthase subunit b′ |
| 3 | 0.1192 | sll0170 | dnaK | 10011001000010001000 | DnaK protein chaperonin |
| 4 | 0.1192 | slr2076 | groEL | 10011001000010001000 | 60kD chaperonin 1 |
| 5 | 0.1192 | sll0998 | lysR | 10011001000010001000 | LysR transcriptional regulator |
| 6 | 0.1192 | sal0020 | petF | 10011001000010001000 | ferredoxin |
| 7 | 0.1192 | ssr2831 | psaE | 10011001000010001000 | photosystem I subunit IV |
| 8 | 0.1192 | sll0819 | psaF | 10011001000010001000 | photosystem I subunit III |
| 9 | 0.1192 | sll1398 | psbW | 10011001000010001000 | photosystem II 13 kD protein |
| 10 | 0.1192 | sll0258 | ptbV | 10011001000010001000 | cytochrome c550 |
| 11 | 0.1192 | sml0007 | psbY | 10011001000010001000 | photosystem II PsbY protein |
| 12 | 0.1192 | slr0012 | rbcS | 10011001000010001000 | ribulose bisphosphate carboxylase small sub. |
| 13 | 0.1192 | sll1744 | rpl1 | 10011001000010001000 | 50S ribosomal protein L1 |
| 14 | 0.1192 | sll1799 | rpl3 | 10011001000010001000 | 50S ribosomal protein L3 |
| 15 | 0.1192 | sll1810 | rpl6 | 10011001000010001000 | 50S ribosomal protein L6 |
| 16 | 0.1192 | sll1743 | rpl11 | 10011001000010001000 | 50S ribosomal protein L11 |
| 17 | 0.1192 | sll1811 | rpl18 | 10011001000010001000 | 50S ribosomal protein L18 |
| 18 | 0.1192 | sll1812 | rps5 | 10011001000010001000 | 30S ribosomal protein S5 |
| 19 | 0.1192 | sll1767 | rps6 | 10011001000010001000 | 30S ribosomal protein S6 |
| 20 | 0.1192 | sll1102 | rps10 | 10011001000010001000 | 30S ribosomal protein S10 |
| 21 | 0.1192 | sll1816 | rps13 | 10011001000010001000 | 30S ribosomal protein S13 |
| 22 | 0.1192 | sal3437 | rps17 | 10011001000010001000 | 30S ribosomal protein S17 |
| 23 | 0.1192 | sll1814 | secY | 10011001000010001000 | preprotein translocase subunit Y |
| 24 | 0.1192 | slr0075 | ycf16 | 10011001000010001000 | ABC transporter subunit |
| 25 | 0.1192 | slr0399 | ycf39 | 10011001000010001000 | hypothetical protein |
| Branch Red algae (and CyaPar) | |||||
| 1 | 0.0712 | slr2067 | apcA | 10011000000000001000 | allophycocyanin a chain |
| 2 | 0.0712 | slr1986 | apcB | 10011000000000001000 | allophycocyanin b chain |
| 3 | 0.0712 | slr0335 | apcE | 10011000000000001000 | phycobilisome LCM core-membrane linker prot. |
| 4 | 0.0712 | slr0611 | sds | 10011000000000001000 | solanesyl diphosphate synthase |
| 5 | 0.0712 | slr0055 | trpG | 10011000000000001000 | anthranilate synthase component II |
| 6 | 0.0712 | slr2032 | ycf23 | 10011000000000001000 | hypothetical protein |
| Branch Nongreen algae (but no CyaPar) | |||||
| 1 | 0.1460 | — | cfxQ | 00010001000010001000 | rubisco expression protein |
| 2 | 0.1339 | — | ycf | 00010001000000001000 | hypothetical protein |
| 3 | 0.1192 | slr0228 | ftsH | 10010001000010011000 | cell division protein |
| 4 | 0.1192 | sll0020 | clpC | 10010001000010001010 | ATP-dep. translocation rel. protease, regulator |
| 5 | 0.1306 | sal2084 | acp | 10010001000010001000 | acyl carrier protein |
| 6 | 0.1306 | slr0833 | dnaB | 10010001000010001000 | replicative DNA helicase |
| 7 | 0.1306 | slr0737 | psaD | 10010001000010001000 | photosystem I subunit II |
| 8 | 0.1306 | slr1655 | psaL | 10010001000010001000 | photosystem I subunit XI |
| 9 | 0.1306 | sll1800 | rpl4 | 10010001000010001000 | 50S ribosomal protein L4 |
| 10 | 0.1306 | sll1821 | rpl13 | 10010001000010001000 | 50S ribosomal protein L13 |
| 11 | 0.1306 | sll1807 | rpl24 | 10010001000010001000 | 50S ribosomal protein L24 |
| 12 | 0.1306 | sar2799 | rpl27 | 10010001000010001000 | 50S ribosomal protein L27 |
| 13 | 0.1306 | sal3436 | rpl29 | 10010001000010001000 | 50S ribosomal protein L29 |
| 14 | 0.1306 | sal3445 | rpl31 | 10010001000010001000 | 50S ribosomal protein L31 |
| 15 | 0.1306 | sll0616 | secA | 10010001000010001000 | preprotein translocase subunit A |
| 16 | 0.1306 | sll0194 | ycf43 | 10010001000010001000 | hypothetical protein |
| 17 | 0.1306 | slr2087 | ycf44 | 10010001000010001000 | hypothetical protein |
| Branch Red algae (but no CyaPar) | |||||
| 1 | 0.0822 | sll0728 | accA | 10010000000000001000 | acetyl-CoA carboxylase alpha subunit |
| 2 | 0.0822 | slr0435 | accB | 10010000000000001000 | biotin carboxyl carrier of acetyl-CoA carboxy |
| 3 | 0.0822 | slr1898 | argB | 10010000000000001000 | N-acetylglutamate kinase |
| 4 | 0.0822 | sll1214 | AT103 | 10010000000000001000 | phytochrome-regulated gene |
| 5 | 0.0822 | sll1498 | carA | 10010000000000001000 | carbamoyl-phosphate synthetase subunit A |
| 6 | 0.0822 | slr2051 | cpcG | 10010000000000001000 | phycobilisome rod-core linker polypeptide |
| 7 | 0.0822 | sll0698 | dfr | 10010000000000001000 | drug sensory protein A |
| 8 | 0.0822 | sal0707 | glnB | 10010000000000001000 | nitrogen regulatory protein P-II |
| 9 | 0.0822 | sll1499 | gltB | 10010000000000001000 | ferredoxin-dependent glutamate synthase |
| 10 | 0.0822 | slr0974 | infC | 10010000000000001000 | initiation factor IF-3 |
| 11 | 0.0822 | sll1536 | moeB | 10010000000000001000 | molybdopterin biosynthesis protein |
| 12 | 0.0822 | sll1423 | ntcA | 10010000000000001000 | global nitrogen regulator |
| 13 | 0.0822 | slr1934 | pdhA | 10010000000000001000 | pyruvate dehydrogenase E1 component α sub |
| 14 | 0.0822 | sll1796 | petJ | 10010000000000001000 | cytochrome c553 |
| 15 | 0.0822 | slr0966 | trpA | 10010000000000001000 | tryptophan synthase α chain |
| 16 | 0.0822 | slr0623 | trxA | 10010000000000001000 | thioredoxin |
| 17 | 0.0822 | slr1780 | ycf | 10010000000000001000 | hypothetical protein |
| 18 | 0.0822 | sll1737 | ycf | 10010000000000001000 | hypothetical protein |
| 19 | 0.0822 | sll0558 | ycf | 10010000000000001000 | hypothetical protein |
| 20 | 0.0822 | sll1879 | ycf | 10010000000000001000 | hypothetical protein |
| Branch EugGra | |||||
| 1 | 0.0731 | — | ycf | 00000010000000000010 | hypothetical protein |
| 2 | 0.0731 | slr0913 | ycf | 10000010000000000000 | hypothetical protein |
| 3 | 0.0731 | slr0914 | ycf | 10000010000000000000 | hypothetical protein |
| Branch Green algae | |||||
| 1 | 0.1373 | sll1833 | fts1 | 10000000011000000000 | penicillin-binding protein |
| 2 | 0.1373 | slr1972 | ycf | 10000000011000000000 | hypothetical protein |
| 3 | 0.1333 | slr1455 | cysA | 10100000111000000000 | sulfate transport system permease protein |
| 4 | 0.1333 | slr1453 | cysT | 10100000111000000000 | sulfate transport system permease protein |
| 5 | 0.1064 | sll0289 | minD | 10100001011000000000 | septum site-determining protein |
| 6 | 0.1054 | slr0772 | chlB | 10101000111000011000 | protochlorophyllide reductase subunit B |
| 7 | 0.1054 | slr0749 | chlL | 10101000111000011000 | light-indep. protochlorophyllide reductase Fe |
| 8 | 0.0899 | slr0750 | chlN | 10101000011000011000 | protochlorophillide reductase subunit N |
| 9 | 0.0979 | sll1463 | ftsH | 10100000101000000000 | cell division protein |
| Branch Land plants | |||||
| 1 | 0.1017 | — | petL | 01000000101101110101 | cytochrome b6-f subunit VI |
| 2 | 0.1006 | — | ycf2 | 01000100000101000001 | hypothetical protein |
| 3 | 0.0965 | — | matK | 01000110100101110101 | maturase K |
| 4 | 0.0813 | — | ycf1 | 01100100111101010100 | hypothetical protein |
| 5 | 0.0970 | slr1281 | ndhJ | 11000000110101100101 | NADH dehydrogenase subunit J |
| 6 | 0.0921 | sll0519 | ndhA | 11000000111101100101 | NADH dehydrogenase subunit 1 |
| 7 | 0.0921 | sll0223 | ndhB | 11000000111101100101 | NADH dehydrogenase subunit 2 |
| 8 | 0.0921 | slr1279 | ndhC | 11000000111101100101 | NADH dehydrogenase subunit 3 |
| 9 | 0.0921 | slr0331 | ndhD | 11000000111101100101 | NADH dehydrogenase subunit 4 |
| 10 | 0.0921 | sll0522 | ndhE | 11000000111101100101 | NADH dehydrogenase subunit 4L |
| 11 | 0.0921 | slr0844 | ndhF | 11000000111101100101 | NADH dehydrogenase subunit 5 |
| 12 | 0.0921 | sll0521 | ndhG | 11000000111101100101 | NADH dehydrogenase subunit 6 |
| 13 | 0.0921 | slr0261 | ndhH | 11000000111101100101 | NADH dehydrogenase subunit 7 |
| 14 | 0.0921 | sll0520 | ndhI | 11000000111101100101 | NADH dehydrogenase subunit I |
| 15 | 0.0921 | slr1280 | ndhK | 11000000111101100101 | NADH dehydrogenase subunit K |
| 16 | 0.0878 | sml0003 | psbM | 11101000101101100101 | photosystem II M protein |
| EpiVir | |||||
| 1 | 0.0169 | — | ycf2 | 01000100000101000001 | hypothetical protein |
| 2 | 0.0119 | — | ycf1 | 01100100111101010100 | hypothetical protein |
| 3 | 0.0119 | — | matK | 01000110100101110101 | maturase K |
| 4 | 0.0119 | ssl3441 | infA | 10100100111000110101 | initiation factor IF-1 |
Genes acting as phylogenetic correlates, as derived from the factor analysis and DP scoring.