Table 1.
Candidate genes and corresponding primers used for qPCR experiments
| Gene | Protein name | C. canephora | GB | ATP | SGN | Primer | Primer sequences | bp |
|---|---|---|---|---|---|---|---|---|
| CaUBQ10 | Ubiquitin | Cc02_g31600 | GW488515 | 32782 | U637098 | BUBI-F BUBI-R |
5’ AAGACAGCTTCAACAGAGTACAGCAT 3’ 5’ GGCAGGACCTTGGCTGACTATA 3’ |
104 |
| CaAEP1 a | Putative aldose 1-epimerase | Cc07_g03170 | GT005185 | 716 | U637659 | 716-1 F 716-1R |
5' CGGTGATGTCCTCTCTGATGAG 3’ 5’ GTTGGGATGAGCTGGTTGTTC 3’ |
75 |
| CaCAB2 a | Chlorophyll a/b-binding protein | Cc09_g09030 | GT003492 | 33540 | U629601 | 48565-F 48565-R |
5’ GTTCAAGGCTGGATCCCAAA 3’ 5’ GCAAGCCCAGATAGCCAAGA 3’ |
100 |
| CaCHI1 a | Class III chitinase | Cc11_g00410 | GT012279 | 32745 | U637166 | 50103-F 50103-R |
5’ AATCAAGCGACCGTCCATTC 3’ 5’ GTGTTTCCGCTGTGGATGTG 3’ |
70 |
| CaCHI2 a | Putative chitinase | Cc00_g14300 | GT011845 | 32737 | U638035 | 53058-F 53058-R |
5’ CCTGCTCGCGGTTTCTACAC 3’ 5’ TTGTTCCAAAAGCCCCATTG 3’ |
70 |
| CaCHI3 a | Chitinase-like protein | Cc03_g13720 | GW491433 | 32875 | U645893 | 23638-F 23638-R |
5’ AAACGGCCCGTCCAGAA 3’ 5’ GCTTTGTCCTGCTGGTCCAT 3’ |
130 |
| CaDLP1 a | Dirigent-like protein | Cc00_g27410 | GW477731 | 35149 | nf | 39577-F 39577-R |
5’ TTGGTAGTCCGGCGAGAGAA 3’ 5’ GCATATCCCCGAGCAAACCT 3’ |
70 |
| CaELIP3 a | Early light-induced protein (ELIP) | Cc03_g04300 | GR985685 | 32771 | U631550 | 32771-F 32771-R |
5’ TCGGTTGCCATGCAATCTT 3’ 5’ GCAGATGAAGCCCACAGCTT 3’ |
100 |
| CaGAS2 a | Glucosyltransferase arbutin synthase | Cc02_g39100 | GT697284 | 3945 | U632419 | 632419-F 632419-R |
5’ GCTGACGACGTTAGGATTGAGA 3’ 5’ AACTTGGCGGTGTCAACCAA 3’ |
101 |
| CaGRP2 a | Glycin-rich protein | Cc00_g16260 | GW430980 | 32799 | U635030 | 53139-1 F 53139-1R |
5’ CACATATGCTGGTGAGCCAAA 3’ 5’ AGGCATTTAAGCGCCATGAT 3’ |
100 |
| CaH2A a | Putative histone H2A | Cc01_g12440 | GT723387 | 33557 | U630412 | 53417-F 53417-R |
5’ GCACTGGAGCTCCGGTCTAC 3’ 5’ AGCAGCATTTCCAGCCAATT 3’ |
80 |
| CaHSP3 a | Heat schock protein (HSP) 70 kDa | Cc02_g08040 | GR982512 | 33197 | U636531 | 33197-1 F 33197-1R |
5’ GGCGTCTGGCAACACGAT 3’ 5’ CGATGAGACGCTCGGTGTCT 3’ |
100 |
| CaIPS1 a | Myo-inositol 1-phosphate synthase | Cc07_g15530 | GT003538 | 10496 | U632517 | 10496-1 F 10496-1R |
5’ AAGCAACCTGAATTTGGCTGAT 3’ 5’ GAGAGGGACCATGGATTCCA 3’ |
100 |
| CaJAMT1 a | Jasmonate O-methyltransferase | Cc03_g07330 | GR989151 | 33008 | U631389 | 47327-F 47327-R |
5’ CTGTGGCTGAACCCTTGCTT 3’ 5’ TCTTTGGACATGCGATCAGAAA 3’ |
100 |
| CaMAS1 a | Momilactone-A synthase | Cc00_g13640 | GW479615 | 33413 | nf | 33413-F 33413-R |
5’ GGGCAGAGGCACGAAAAA 3’ 5’ GGTACCCTGCCGCAACTATG 3’ |
60 |
| CaPP2 a | Putative phloem protein 2 (PP2) | Cc03_g13000 | GR995691 | 33207 | U633544 | 33207-F 33207-R |
5’ GGTGTTGGCGATGTCGAGAT 3’ 5’ TTCCTTGGGTCGAAGCTCAA 3’ |
90 |
| CaPSBB a | Photosystem II CP47 (psbB)-like protein | nf | GW447378 | 22102 | U630312 | 55586-F 55586-R |
5’ ATCGGAAATAATCCGGCAAA 3’ 5’ AACCATCCAATCGCTATTCCA 3’ |
80 |
| CaSAMT1 a | S-adenosyl-methionine-methyltransferase | Cc03_g05630 | DV672716 | 754 | U629783 | 34318-F 34318-R |
5’ AACGTTTGGGTGATGAATGTTG 3’ 5’ GTGCCAATAAGCCCTCTATCGT 3’ |
80 |
| CaSDC1 a | S-adenosyl-L-methionine decarboxylase | Cc11_g11130 | GT002431 | 8508 | U629687 | 8508-1 F 8508-1R |
5’ CTCGATTCCTCCCATCCTGAA 3’ 5’ TGACTGTGCCCCAGGGAATA 3’ |
100 |
| CaSLP1 a | Subtilisin-like protein | Cc00_g19100 | GW430663 | 1620 | nf | 7961-F 7961-R |
5’ CCATCGTTCTCGGTGGTCTT 3’ 5’ GCATTGCTCCCCACATTCTT 3’ |
80 |
| CaSTK1 a | Hypothetical S/T protein kinase | Cc00_g18670 | GT687049 | 6301 | U631794 | 6301-1 F 6301-1R |
5’ CCACCCACAAGCTGTATTCTCA 3’ 5’ GACCCAATGGGATGTCATCAC 3’ |
80 |
| CaUNK1 c | Unknown protein 1 | Cc03_g08880 | DV689820 | 33062 | U614843 | 182052-F 182052-R |
5’ TATAGTGTTTATGGTGTGGCTTTCAGT 3’ 5’ GTACCACCGTAGGGAGACGTATG 3’ |
79 |
| CaUNK2 b | Unknown protein 2 | Cc07_g01940 | DV708962 | 31492 | U637447 | 33353-F 33353-R |
5’ GAACTTACAAACGCGCGTAACC 3’ 5’ CATGGTCGAATCCAGATTTCATT 3’ |
80 |
| CaUNK3 b | Unknown protein 3 | nf | nf | 22823 | nf | 22823-F 22823-R |
5’ GGAAGCATGCACACAGAAAATAGA 3’ 5’ TTCCTGTTTACGTCTTTTTCAATTGA 3’ |
80 |
| CaUNK4 b | Unknown protein 4 | Cc06_g11210 | GW465088 | 39984 | nf | 55677-F 55677-R |
5’ GCTGTGGTTTTAAAGTTTTGATGGA 3’ 5’ TGCAAAATTAAGGTCCCAACAGT 3’ |
81 |
| CaUNK5 b | Unknown protein 5 | Cc08_g09510 | GW474926 | 4578 | nf | 4578-F 4578-R |
5’ GGAGTTCCTGTCCGAAGTTGTT 3’ 5’ GGCATGCTGTCACCTGAAAA 3’ |
80 |
| CaUNK6 b | Unknown protein 6 | Cc03_g06850 | GT002178 | 34993 | U632634 | 34993-F 34993-R |
5’ AAGCCAATGCCGATCGATT 3’ 5’ CGCCGCCGAAGATCTCTAG 3’ |
100 |
| CaUNK7 b | Unknown protein 7 | Cc03_g00560 | GW444736 | 33613 | U631416 | 25639-F 25639-R |
5’ CGAGGAAGCTGAAGGAAAGGA 3’ 5’ TCCGACTGGCCTAACAAGGT 3’ |
61 |
| CaUNK8 b | Unknown protein 8 | Cc00_g04970 | DV695331 | 33190 | U640780 | LP18101-F LP18100-R |
5’ CTCGCGTGGCCGAGATC 3’ 5’ CCCTCACATTTCCACGTGAAT 3’ |
100 |
| CaUNK9 b | Unknown protein 9 | Cc03_g08920 | GT649500 | 32762 | U636808 | 30926-F 30926-R |
5’ CGGAGGAGGCCATGGAGGT 3’ 5’ CCGTGTCCATAACCACCATGT 3’ |
123 |
| CaUNK10 c | Unknown protein 10 | nf | GT648004 | 14813 | U645073 |
D18240-F D18240-R |
5’ TAGCCTTGTTCTTTTAGGGAGTCTTATC 3’ 5’ AGAGCTTCGTCCAGGAAGAAGA 3’ |
134 |
| CaUNK11 b | Unknown protein 11 | Cc03_g14330 | GR991912 | 8598 | U637116 | 32792-F 32792-R |
5’ GCTGGGAAAGCTACAGAAACCA 3’ 5’ GAACTCCAACGCCAAGCATT 3’ |
100 |
| CaUNK12 b | Unknown protein 12 | Cc10_g12840 | nf | 53029 | nf | 53029-F 53029-R |
5’ CTTCACACCATTCAGACAATCGA 3’ 5’ GACCGTAATTGGGCGTCAAT 3’ |
100 |
| CaUNK13 b | Unknown protein 13 | Cc00_g17760 | GT673421 | 14198 | U639484 | 33980-F 33980-R |
5’ ATTGCCCTGTTTGCATGCAT 3’ 5’ CTGCATGGTGATTGTCCTCAGT 3’ |
100 |
| CaUNK14 b | Unknown protein 14 | Cc00_g16260 | GT672564 | 48325 | U635030 | 11524-F 11524-R |
5’ GGCGGTTGTCATGGATACG 3’ 5’ TTTGGCTCACCAGCATATGTG 3’ |
119 |
| CaUNK15 b | Unknown protein 15 | Cc00_g04970 | GR983286 | 33190 | U636790 | 05517-F 05517-R |
5’ AAAATTTCACCACGGCAAGCT 3’ 5’ TTGCCTCCCTCACATTTCCA 3’ |
72 |
| CaUNK16 b | Unknown protein 16 | nf | GW464209 | 9761 | U639049 | 18112-F 18112-R |
5’ TGTGAACTGCCATCCCAAGA 3’ 5’ AAGACTACCATGTCCAACAACTTCAG 3’ |
88 |
| CaUNK17 b | Unknown protein 17 | Cc03_g08920 | GT685623 | 32762 | U636800 | 42747-F 42747-R |
5’ AGGTGGCTGCCAAGTCAGTT 3’ 5’ ATGGTACTTGGCTTCTCCTTCCTC 3’ |
71 |
|
CaLTP1
d
CaLTP2 d |
Non-specific lipid transfer protein (nsLTP) | Cc11_g09700 |
HG008739 HG008740 |
46897 | U632702 | LTP-R2 LTP-FT |
5’ CACCATTACATGGGAACGTTGC 3’ 5’ CTGTGGTCTGAAATGGCCAACT 3’ |
120 |
| CaLTP3 d | Non-specific lipid transfer protein (nsLTP) | Cc04_g06890 | HG008741 | 33368 | U632702 | LTP-R1 LTP-FT |
5’ ATTCAACACCATTACTAGTTTTCGAGC 3’ 5’ CTGTGGTCTGAAATGGCCAACT 3’ |
113 |
| LTP d | nf | - | U632702 | LTP-F100 LTP-R100 |
5’ TGCAATTTTATCAAAGATCCAGC 3’ 5’ AGTTGGCCATTTCAGACCACA 3’ |
93 |
Gene names were assigned based on the best BLAST hit obtained by comparing the coffee ESTs with public databases. C. canephora means coffee sequences that aligned with the candidate genes using BLASTx searches against NR/NCBI and filtration (http://coffee-genome.org [59]). GenBank (GB: http://blast.ncbi.nlm.nih.gov/Blast.cgi), ATP (http://www.lge.ibi.unicamp.br/cirad/) and SGN (Sol Genomics Network, http://solgenomics.net/) accession numbers of coffee ESTs are also given, as well as the length of base pairs (bp) of amplicons. nf: no-hits found (SGN: tools/blast/SGN Clusters [current version] / Coffee species Clusters, GB: BLASTn/Nucleotide collection [nr/nt]). The size of amplicons is based on the unigene. (a): candidate genes (n = 20) identified during this study. (b): orphan genes (n = 14) previously described [35] and analysed in this study. (c): orphan genes (n = 3) with expression already been studied in leaves of DT and DS clones of C. canephora conilon [10, 11, 36]. (d): LTP-encoding genes were previously described [37]