Table II. Comparative analysis between S. lycopersicum and S. pennellii orthologous genomic regions.
Sl, S. lycopersicum; Sp, S. pennellii; At, Arabidopsis; CB, total of compared bases; ND, not determined; UD, undetermined because dn = 0.
| BIN | IDa | Nameb | Identity (InDels)c CB: XXX |
Exonsd | Lengthe (Amino Acids) | Amino Acid Polymorphismsf |
ds/dng |
|||
| Exons | Introns | Sl-Sp | Sl-At | Sp-At | ||||||
| 41 | Sp04gBP4C04.1 | Diphthine synthase | 99 (0) CB: 100 | 1h | 33i | 0 | ||||
| Sp04gBP4C04.2 | Putative chaperone protein DNAJ-related | 99 (0) CB: 480 | 95.3 (2.7) CB: 2,224 | 5 | 159 | 2 | 5.3 | 7.2j | 7.5j | |
| Sp04gBP4C04.3 | Expressed gene 1 | 98.6 (0) CB: 633 | 94.9 (1.1) CB: 2,077 | 7 | 179 | 4 | ||||
| Sp04gBP4C04.4 | Abscisic acid-responsive HVA22 family protein | 98.4 (0.0) CB: 966 | 96.0 (1.5) CB: 1,202 | 6 | 321 | 9 | 1.83 | 2.23j | 2.15j | |
| Sp04gBP4C04.5 | E2F transcription factor | 98.8 (0) CB: 996 | 94.3 (3.3) CB: 5,294 | 10 | 331 | 8 | ||||
| Sp04gBP4C04.6 | Putative eukaryotic initiation factor 3 γ-subunit family protein | 98.7 (0) CB: 1,341 | 95.3 (3.1) CB: 4,320 | 13 | 446 | 7 | 3.0 | 3.12j | 3.11j | |
| Sp04gBP4C04.7 | Putative zinc finger (C2H2 type) family protein | 97.6 (0.4) CB: 1,359 | 91.4 (5.0) CB: 1,865 | 4 | 451 | 13 | 3.8j | 3.9j | 3.9j | |
| Sp04gBP4C04.8 | Plastidic hexokinase | 99.2 (0) CB: 1,500 | 88.8 (8.1) CB: 2,111 | 9 | 499 | 2 | 11j | 4.6j | 4.6j | |
| Sp04gBP4C04.9 | Putative clathrin assembly protein AP17-like protein | 100 (0) CB: 429 | 73.1(25.2) CB: 3,113 | 6 | 142 | 0 | UD | 17.8j | 17.8j | |
| Sp04gBP4C04.10 | Expressed gene 2 | 96.5 (0.6) CB: 909 | 1 | ND | ND | |||||
| Sp04gBP4C04.11 | Expressed gene 3 | 98.3 (0.3) CB: 1,851 | 96.7 (1.6) CB: 1,684 | 10 | 608 | 9 | ||||
| Sp04gBP4C04.12 | Putative transcription coactivator-like protein | 99.4 (0) CB: 507 | 96.2 (2.2) CB: 1,604 | 5 | 168 | 0 | UD | 8.7j | 8.7j | |
| Sp04gBP4C04.13 | β-Fructofuranosidase | 99.2 (0) CB: 1,713 | 91.2 (6.1) CB: 2,008 | 4 | 570 | 1 | 26j | 8.0j | 7.7j | |
| Sp04gBP4C04.14 | Putative cytomatrix protein | 99 (0) CB: 1,062 | 94 (3.8) CB: 1,796 | 4 | 353 | 8 | 1.1 | 1.3 | 1.3 | |
| 7H | Sp07gCP5C04.1 | Glycerophosphoryl diester phosphodiesterase family protein | 98.8 (0.0) CB: 162 | 95.9 (1.9) CB: 1,025 | 2h | 54i | 2 | |||
| Sp07gCP5C04.2 | Protease inhibitor/seed storage/lipid transfer protein family protein | 97.8 (0.0) CB: 315 | 1 | 104 | 5 | 1.04 | 1.99j | 1.95j | ||
| Sp07gCP5C04.3 | Polygalacturonase-inhibiting protein 1 (PGIP1) | 97.7 (0.0) CB: 984 | 1 | 327 | 6 | 5.8j | 4.1j | 3.6j | ||
| Sp07gCP5C04.4 | Similar to fimbrin-like protein | 98.8 (0.0) CB: 2,571 | 97.0 (1.5) | 12 | 856 | 0 | UD | 7.3j | 7.4j | |
| Sp07gCP5C04.5 | Expressed gene 1 | 96.9 (1.3) CB: 669 | 1 | ND | ND | |||||
| Sp07gCP5C04.6 | Wax synthase isoform 3 | 86.8 (11.1) CB: 1,053 | 1 | 350 | 53 | 2 | 2.07j | 2.06j | ||
| Sp07gCP5C04.7 | Wax synthase isoform 3 | 98.4 (0.0) CB: 1,035 | 1 | 344 | 10 | 1.9 | 2.1j | 2.0j | ||
| Sp07gCP5C04.8 | Cell division protein FtsZ | 99.0 (0.0) CB: 1,254 | 95.1 (2.2) CB: 3,438 | 6 | 417 | 1 | 15.5j | 6.0j | 6.3j | |
| Sp07gCP5C04.9 | TATA-binding protein-associated factor | 99.3 (0.0) CB: 1,734 | 96.5 (1.8) CB: 2,580 | 12 | 577 | 9 | 0.87 | 2.9j | 2.9j | |
| Sp07gCP5C04.10 | Similar to syntaxin 52 (SYP52) | 94.8 (4.8) CB: 735 | 94.9(2.8) CB: 2,427 | 5 | 243 | 11 | ||||
| Sp07gCP5C04.11 | Ser/Thr protein phosphatase | 99.5(0.0) CB: 918 | 96.1 (1.1) CB: 5,494 | 8 | 305 | 1 | 8.0 | 29.8j | 32.6j | |
| Sp07gCP5C04.12 | Lipid-binding serum glycoprotein family protein | 98.8 (0.0) CB: 1,302 | 95.1 (2.3) CB: 2,731 | 5 | 433 | 8 | 1.9 | 2.1j | 2.2j | |
| Sp07gCP5C04.13 | PHD finger family protein | 98.1 (0.1) CB: 2,184 | 98.2 (0.3) CB: 1,150 | 3 | 727 | 24 | ||||
| Sp07gCP5C04.14 | S-Adenosyl-l-Met:carboxyl methyltransferase family protein | 99.1 (0.0) CB: 1,155 | 80.1 (11.7) CB: 1,222 | 4 | 384 | 3 | 5.5 | 7.0j | 6.6j | |
| Sp07gCP5C04.15 | Hyp-rich glycoprotein family protein | 96.5 (1.2) CB: 964 | 91.8 (3.1) CB: 1,397 | 3h | 295i | 23 | ||||
| 11C | Sp11gBP4E08.1 | Tetratricopeptide repeat-containing protein | 98.7 (0.0) CB: 476 | 97.0 (1.6) CB: 507 | 3h | 158i | 3 | |||
| Sp11gBP4E08.2 | Expressed gene 2 | 99.4 (0.0) CB: 360 | 93.8 (4.3) CB: 5,444 | 2 | 119 | 1 | 2.7 | 2.9j | 3.0j | |
| Sp11gBP4E08.3 | Glc-6-P/phosphate translocator-related | 98.2 (0.0) CB: 1,014 | 93.8 (1.2) CB: 1,376 | 5 | 337 | 9 | 2.6 | 7.03j | 7.04j | |
| Sp11gBP4E08.4 | Peptidoglycan-binding LysM domain-containing protein | 98.9 (0.0) CB: 1,237 | 94.7 (2.2) CB: 1,692 | 5 | 413 | 11 | 1.2 | 4.1j | 4.2j | |
| Sp11gBP4E08.5 | Coiled-coil protein | 98.8 (0.0) CB: 2,013 | 96.0 (2.8) CB: 2,106 | 4 | 670 | 11 | 3.8j | 1.5j | 1.5j | |
| Sp11gBP4E08.6 | CH1 (chlorophyll b biosynthesis); chlorophyllide a oxygenase | 98.9 (0.0) CB: 1,612 | 95.4 (1.5) CB: 2,203 | 9 | 536 | 2 | 16.5j | 6.6j | 6.8j | |
| Sp11gBP4E08.7 | BTB/POZ domain-containing protein | 99.8 (0.0) CB: 987 | 95.1 (2.7) CB: 1,812 | 4 | 329 | 1 | 4.0 | 6.5j | 6.3j | |
| Sp11gBP4E08.8 | F-box family protein | 99.3 (0.0) CB: 990 | 96.5 (1.1) CB: 7,288 | 11 | 330 | 3 | 3.9 | 6.1j | 6.1j | |
| Sp11gBP4E08.9 | Putative replication factor C 37-kD subunit | 98.4 (0.0) CB: 1,020 | 78.6 (16.8) CB: 10,653 | 12 | 340 | 1 | 54.0j | 8.0j | 7.6j | |
a
Gene identification.
b
Gene functional identity.
c
Percentage of identity and InDels between the S. lycopersicum and S. pennellii regions analyzed.
d
Number of exons compared between both genotypes.
e
Number of amino acids compared between both genotypes.
f
Polymorphic amino acids on the predicted protein sequence.
g
Synonymous distance/nonsynonymous distance.
h
Exons not included in the comparative evolutionary analysis of S. pennellii and S. lycopersicum orthologous regions.
i
Only partial sequences were compared because genes were located at the end of the clones for any of the genotypes.
j
Statistically significant purifying selection (P < 0.05).