Comparative Analysis of Chloroplast Genomes: Functional Annotation, Genome-Based Phylogeny, and Deduced Evolutionary Patterns

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.

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  1. Genome Res. 12: 567-583

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