Table 1. Lhcf, Lhcr, Lhcx, and FCP genes identified in C. cryptica CCMP332 using T. pseudonana and C. meneghiniana 1020-1a gene sequences.
In cases where identical gene models exist at several loci, only one gene name is given. In cases where different gene predictions for one locus are present in the database, the models with the least resemblance to their T. pseudonana counterparts are shown in italics and named ‘a’ and ‘b’. Fcp genes of C. meneghiniana are according to Eppard and Rhiel (1998) and Eppard et al. (2000). Dashes indicate no gene identifier available in database.
| Name | Gene Identifier | Location | Mature Protein |
|---|---|---|---|
| Lhcf | |||
| CcLhcf1.1a | g17931.t1 | g009304_00092:845-1770 | Lhcf1 = Fcp1-3 |
| g25998.t1 | g002362_00144:845-1770 | ||
| g26023.t1 | g002346_00143:1116-2041 | ||
| CcLhcf1.2a | g11743.t1 | g017983_00088:3722-4321 | Lhcf1 = Fcp1-3 |
| g9813.t1 | g021620_00082:470-1069 | ||
| g21457.t1 | g005884_00107:470-1069 | ||
| CcLhcf3b | g27206.t1 | g001521_00091:7-495 | Lhcf3 |
| Fcp5b | Not found | Fcp5 | |
| CcLhcf4 | g4695.t1 | g037374_00040:1988-2593 | Lhcf4 |
| CcLhcf6 | g20180.t1 | g007028_00058:2475-3077 | Lhcf6 |
| CcLhcf6a | — | g007028_00058:2475-3219 | |
| CcLhcf10 | g1413.t1 | g068182_00128:55071-55679 | Lhcf10 |
| CcLhcf11 | g9270.t1 | g022704_00101:7497-8159 | Lhcf11 |
| Lhcr | |||
| CcLhcr1 | g4191.t1 | g039603_00095:12747-13619 | Lhcr1 |
| CcLhcr2 | g17037.t1 | g010304_00068:3475-3987 | Lhcr2 |
| CcLhcr2a | g13001.t1 | g010304_00068:3478-4257 | |
| CcLhcr2b | — | g010304_00068:3238-4373 | |
| CcLhcr3c | g22357.t1 | g005177_00041:3338-4286 | Lhcr3, similar to |
| CcLhcr3a | — | g005177_00041:3112-4460 | Fcp4 |
| CcLhcr3b | — | g005177_00041:3338-4286 | |
| CcLhcr5 | g12115.t1 | g017270_00043:10106-10888 | Lhcr5 |
| CcLhcr5a | g9253.t1 | g017270_00043:10109-11167 | |
| CcLhcr5b | — | g017270_00043:10106-11252 | |
| CcLhcr7 | g15657.t1 | g012035_00070:5433-6183 | Lhcr7 |
| CcLhcr8.1 | g25826.t1 | g00250_00057:1026-1894 | Lhcr8.1 |
| CcLhcr8.2 | g22748.t1 | g004863_00062:1-677 | Lhcr8.2 |
| CcLhcr11 | g10947.t1 | g019362_00072:17991-18731 | Lhcr11 |
| CcLhcr14 | g18288.t1 | g008875_00105:6649-7349 | Lhcr14 |
| Lhcx | |||
| CcLhcx1.1d | g2066.t1 | g059009_00077:10108-10839 | Lhcx1.1 |
| CcLhcx1.2d | g14788.t1 | g013146_00085:3526-4158 | Lhcx1.2 = Fcp6, 8, 9 |
| CcLhcx5e | g21285.t1 | g006023_00084:4427-5140 | Lhcx5, similar to |
| CcLhcx5a | g16306.t1 | g006023_00084:4430-5454 | Fcp12 |
| CcLhcx6 | g14787.t1 | g013146_00085:2016-2768 | Lhcx6 |
| CcLhcx6a | g11298.t1 | g013146_00085:1957-2768 | |
| CcLhcx6_1 | g10346.t1 | g020598_00076:14804-15523 | Lhcx6_1 |
| CcLhcx6_1a | g7882.t1 | g020598_00076:14657-15523 | |
| FCP | |||
| CcFCP3 | g6093.t1 | g025849_00094:2456-3409 | FCP3 |
| CcFCP5 | g12200.t1 | g017153_00078:12827-14314 | FCP5 |
| CcFCP10 | g4274.t1 | g039269_00091:21945-22616 | FCP10 |
Lhcf1 genes are identical to Fcp1-3 except for the N-terminal presequences, where only Lhc1.2 is identical to Fcp2 (see Supplemental Fig. S1).
Lhcf3 encodes for a protein that is identical to Fcp5 except for two amino acid exchanges and a shorter N-terminal presequence in case of Lhcf3 (see Supplemental Fig. S1). Fcp5 is listed as well because both Lhcf3 and Fcp5 were identified by MS in the FCP complexes of C. meneghiniana (Tables 2 and 3), but only CcLhcf3 is present in the C. cryptica CCMP332 genome.
Different predictions for Lhcr3 have different insertions, but are most comparable with Fcp4 (see Supplemental Fig. S1).
Lhcx1.1 codes for a protein that has a one amino acid deletion compared with Lhcx1.2. Lhcx1.2 is identical to Fcp6, 8, 9 and almost identical to Fcp7 (in the protein five amino acids are exchanged, four of them in the presequence; see Supplemental Fig. S1).
Lhcx5 is most similar to Fcp12, but the N terminus of the protein is six amino acids longer, and in total five amino acids are exchanged (four of them in presequence; see Supplemental Fig. S1).