Table 2.
Identification of ABCDE candidate genes in C. sativa.
| Class from ABCDE model | Cannabis sativa (GCA_900626175.1) best hitagainst V. vinifera and A. thalianaMADS-box TFs (BLASTp) | Vitis vinifera (PN40024 v1 ID) | Arabidopsis thaliana (Araport11) | Transcripts (GIFP00000000.1)corresponding to theGCA_900626175.1 proteins | Correspondence between GIFP00000000.1 transcripts andSRP006678/SRP008673 |
|---|---|---|---|---|---|
| Class A | Cs_CAULIFLOWER_A X1 (XP_030481490), Cs_CAULIFLOWER_A X2 (XP_030481491) |
VviAP1 (VIT_01s0011g00100) | At_AP1/AGL7 (AT1G69120) | Cannbio_054734 | PK21815.1 |
| Cs_CAULIFLOWER_A-like_1 (XP_030485608), Cs_CAULIFLOWER_A-like_2 (XP_030485101) |
VviFUL1 (VIT_17s0000g04990) | At_FUL/AGL8 (AT5G60910) | Cannbio_008529, Cannbio_059606 |
PK19698.1, PK01844.1 | |
| Class B | Cs_TM6 (XP_030499268) | VviAP3a (VIT_18s0001g13460), VviAP3b/VvTM6 (VIT_04s0023g02820) |
At_AP3 (AT3G54340) | Cannbio_014948 | n.a. |
| Cs_MADS_2-like (XP_030484132), Cs_MADS_2-like_X1 (XP_030482855), Cs_MADS_2-like_X2 (XP_030482856) |
VviPI/VvMADS9 (VIT_18s0001g0176) | At_PI (AT5G20240) | Cannbio_009872 | PK22420.1 | |
| Class B-sister | Cs_FBP24_X1 (XP_030484437), Cs_FBP24_X2 (XP_030484436), Cs_FBP24-like_X1 (XP_030490979) |
VviABS1 (VIT_10s0042g00820), VviABS2 (VIT_01s0011g01560), VviABS3 VIT_02s0025g02350 |
At_TT16/ABS (AT5G23260) | Cannbio_013942, Cannbio_063474 |
PK26778.1, |
| Class C | Cs_AGAMOUS-like (XP_030480504), Cs_MADS1 (XP_030481705) |
VviAG1/MADS1 (VIT_12s0142g00360), VviAG2 (VIT_10s0003g02070) |
At_SHP1/AGL1 (AT3G58780), At_AG (AT4G18960) |
Cannbio_055846, Cannbio_057002 |
PK20142.1, PK03292.1 |
| Cs_MADS3_1 (XP_030487367), Cs_MADS3_2 (XP_030500965) |
VviAGL6a/MADS3 (VIT_15s0048g01270), VviAGL6b (VIT_16s0022g02330) |
At_AGL6 (AT2G45650) | Cannbio_062689, Cannbio_050725 |
PK14825.1, PK13658.1 | |
| Class D | Cs_AGAMOUS-like (XP_030480504), Cs_MADS1 (XP_030481705) |
VviAG3/VvMADS5 (VIT_18s0041g01880) | At_STK/AGL11 (AT4G09960) | Cannbio_055846, Cannbio_057002 |
PK20142.1, PK03292.1 |
| Class E | Cs_MADS2_X1_1 (XP_030484352), Cs_MADS2_X1_2 (XP_030492901), Cs_MADS2_X2_1 (XP_030484353), Cs_MADS2_X2_2 (XP_030492902), Cs_MADS2_X2_3 (XP_030484350), Cs_MADS4 (XP_030496177) |
VviSEP1/VvMADS2 (VIT_14s0083g01050), VviSEP2 (VIT_17s0000g05000), VviSEP3/VviMADS4 (VIT_01s0010g03900), VviSEP4 (VIT_01s0011g00110) |
At_ SEP1/AGL2 (AT5G15800), At_ SEP2/AGL4 (AT3G02310), At_ SEP3/AGL9 (AT1G24260), At_ SEP4/AGL3 (AT2G03710) |
Cannbio_012895, Cannbio_052937, |
PK08909.1, PK19420.1 |
By means of a BLASTp alignment against the ABCDE proteins of V. vinifera and A. thaliana, the candidate ABCDE proteins of C. sativa were retrieved from the representative proteome (GCA_900626175.1). The corresponding transcripts were then searched through a tBLASTn approach, aligning the candidate ABCDE proteins against the cannabis transcriptome shotgun assembly (GIFP00000000.1). Finally, to evaluate the expression levels of the putative ABCDE proteins in different tissues of two different cannabis strains (Finola and Purple Kush, SRP006678, and SRP008673, respectively), a BLASTn approach was applied, aligning the GIFP00000000.1 transcripts to the abovementioned RNA-seq experiments (SRP006678 and SRP008673).