Table 1. 27 Lhc superfamily genes identified in jatropha.
| Subfamily | Gene name | Locus ID | Scaffold position | Nucleotide length (bp, from start to stop codons) | Intron no. | EST no. | AA | TP length | TMH | Ortholog | OG | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CDS | Gene | Rc | Me | At | ||||||||||
| Lhca | JcLhca1 | JCGZ_23938 | scaffold794:74368-75803(−) | 738 | 1,076 | 3 | 0 | 245 | 45 | 3 | RcLhca1 | MeLhca1.1 MeLhca1.2 |
AtLhca1 | Lhca1 |
| JcLhca2 | JCGZ_17961 | scaffold502:3176588-3178724(+) | 813 | 1,491 | 4 | 1 | 270 | 58 | 3 | RcLhca2 | MeLhca2.1 MeLhca2.2 |
AtLhca2 | Lhca2 | |
| JcLhca3 | JCGZ_15032 | scaffold42:178242-179765(−) | 816 | 1,171 | 2 | 8 | 271 | 38 | 3 | RcLhca3 | MeLhca3 | AtLhca3 | Lhca3 | |
| JcLhca4 | JCGZ_11643 | scaffold328:2197266-2195814(−) | 750 | 917 | 2 | 2 | 249 | 48 | 3 | RcLhca4 | MeLhca4.1 MeLhca4.2 |
AtLhca4 | Lhca4 | |
| JcLhca5 | JCGZ_04265 | scaffold159:84206-85704(+) | 795 | 1,255 | 5 | 0 | 264 | 57 | 3 | RcLhca5 | MeLhca5 | AtLhca5 | Lhca5 | |
| JcLhca6 | JCGZ_07509 | scaffold211:3089530-3091440(−) | 792 | 1,612 | 4 | 0 | 263 | 42 | 3 | RcLhca6 | MeLhca6 | AtLhca6 | Lhca6 | |
| Lhcb | JcLhcb1.1 | JCGZ_04588 | scaffold160:101030-101541(+) | 798 | 798 | 0 | 28 | 265 | 35 | 3 | RcLhcb1.1 RcLhcb1.2 RcLhcb1.3 |
MeLhcb1.1 MeLhcb1.2 MeLhcb1.3 |
AtLhcb1.1 AtLhcb1.2 AtLhcb1.3 AtLhcb1.4 AtLhcb1.5 |
Lhcb1 |
| JcLhcb1.2 | JCGZ_04587 | scaffold160:97668-99902(−) | 798 | 798 | 0 | 17 | 265 | 35 | 3 | RcLhcb1.1 RcLhcb1.2 RcLhcb1.3 |
MeLhcb1.1 MeLhcb1.2 MeLhcb1.3 |
AtLhcb1.1 AtLhcb1.2 AtLhcb1.3 AtLhcb1.4 AtLhcb1.5 |
Lhcb1 | |
| JcLhcb2 | JCGZ_18481 | scaffold529:239615-242657(−) | 798 | 2,225 | 1 | 10 | 265 | 37 | 3 | RcLhcb2 | MeLhcb2.1 MeLhcb2.2 |
AtLhcb2.1 AtLhcb2.2 AtLhcb2.3 |
Lhcb2 | |
| JcLhcb3 | JCGZ_00703 | scaffold108:360030-361580(−) | 804 | 1,202 | 2 | 5 | 267 | 44 | 3 | RcLhcb3 | MeLhcb3 | AtLhcb3 | Lhcb3 | |
| JcLhcb4 | JCGZ_25025 | scaffold843:295347-296708(+) | 858 | 957 | 1 | 8 | 285 | 31 | 3 | RcLhcb4 | MeLhcb4 | AtLhcb4.1 AtLhcb4.2 |
Lhcb4 | |
| JcLhcb8 | JCGZ_01281 | scaffold11:738853-741122(+) | 840 | 1,786 | 1 | 0 | 279 | 31 | 3 | RcLhcb8 | MeLhcb8 | AtLhcb8 | Lhcb8 | |
| JcLhcb5 | JCGZ_06701 | scaffold200:160436-162429(−) | 876 | 1,573 | 5 | 1 | 291 | 41 | 3 | RcLhcb5 | MeLhcb5 | AtLhcb5 | Lhcb5 | |
| JcLhcb6 | JCGZ_20203 | scaffold645:375633-376811(+) | 765 | 844 | 1 | 1 | 254 | 49 | 3 | RcLhcb6 | MeLhcb6 | AtLhcb6 | Lhcb6 | |
| JcLhcb7 | JCGZ_08016 | scaffold221:188978-192485(−) | 1,014 | 3,050 | 5 | 0 | 337 | 52 | 3 | RcLhcb7 | MeLhcb7 | AtLhcb7 | Lhcb7 | |
| PsbS | JcPsbS | JCGZ_12094 | scaffold339:857142-859344(−) | 825 | 1,726 | 3 | 2 | 274 | 62 | 4 | RcPsbS | MePsbS | AtPsbS | PsbS |
| ELIP | JcELIP | JCGZ_02231 | scaffold119:1376949-1378080(−) | 585 | 808 | 2 | 6 | 194 | 86 | 3 | RcELIP | MeELIP | AtELIP1 AtELIP2 |
ELIP |
| OHP | JcOHP1 | JCGZ_09105 | scaffold250:2426033-2426931(−) | 357 | 552 | 2 | 2 | 118 | 48 | 1 | RcOHP1 | MeOHP1 | AtOHP1 | OHP1 |
| JcOHP2 | JCGZ_08332 | scaffold224:432321-435041(+) | 552 | 2,339 | 1 | 0 | 183 | 47 | 1 | RcOHP2 | MeOHP2.1 MeOHP2.2 |
AtOHP2 | OHP2 | |
| SEP | JcSEP1 | JCGZ_23193 | scaffold7:432788-436707(−) | 438 | 3,498 | 3 | 3 | 145 | 71 | 2 | RcSEP1 | MeSEP1 | AtSEP1 | SEP1 |
| JcSEP2 | JCGZ_09398 | scaffold255:592063-593949(+) | 582 | 1,322 | 1 | 0 | 193 | 46 | 2 | RcSEP2 | MeSEP2 | AtSEP2 | SEP2 | |
| JcSEP3 | JCGZ_03488 | scaffold137:779011-781250(+) | 780 | 1,919 | 2 | 4 | 259 | 100 | 2 | RcSEP3 | MeSEP3.1 MeSEP3.2 |
AtSEP3.1 AtSEP3.2 |
SEP3 | |
| JcSEP6 | JCGZ_26324 | scaffold906:2486216-2487759(−) | 759 | 932 | 2 | 0 | 252 | 88 | 2 | RcSEP6 | MeSEP6 | – | SEP6 | |
| JcSEP4 | JCGZ_06634 | scaffold20:991705-992601(+) | 570 | 570 | 0 | 0 | 189 | 56 | 2 | RcSEP4 | MeSEP4 | AtSEP4 | SEP4 | |
| JcSEP5 | JCGZ_07816 | scaffold211:5206555-5210867(−) | 447 | 3,909 | 4 | 0 | 148 | 75 | 1 | RcSEP5 | MeSEP5 | AtSEP5 | SEP5 | |
| Psb33 | JcPsb33 | JCGZ_17235 | scaffold5:830004-833169(+) | 867 | 2,803 | 2 | 1 | 288 | 62 | 1 | RcPsb33 | MePsb33.1 MePsb33.2 |
AtPsb33 | Psb33 |
| FCII | JcFCII | JCGZ_24260 | scaffold813:61000-71385(−) | 1,500 | 9,600 | 9 | 0 | 499 | 86 | 1 | RcFCII | MeFCII | AtFCII | FCII |
Notes.
- AA
- amino acid
- At
- Arabidopsis thaliana
- bp
- base pair
- CDS
- coding sequence
- EST
- expressed sequence tag
- Me
- Manihot esculenta
- OG
- orthologous group
- Rc
- Ricinus communis
- TMH
- transmembrane helix
- TP
- transit peptide)