Fig 1.
a. Vesicle trafficking occurring between the endosome and trans-Golgi, facilitated by the COG complex. b. Components of the COG complex.
Table 1.
G. max COG syncytium gene expression summary.
Table 2.
COG paralogs in select plant species.
Table 3.
COG genes that have experienced duplication in the studied plants.
Fig 2.
COG RNA seq expression abundance in different tissue types in G. max.
* along with the red arrowhead indicates the gene functions in defense (Lawaju et al. 2020 [17]). In this image, the spice variants are labeled. For example, COG7-2-a is Glyma.12G013000.1, COG7-2-b is Glyma.12G013000.2 and COG7-2-c is Glyma.12G013000.3. COG7-2-b is Glyma.12G013000.2 is the examined splice variant that functions in defense (Lawaju et al. 2020 [17]). Gene expression data has been obtained from Phytomine in Phytozome (Libult et al. 2010; Goodstein et al. 2012 [49]; Wang et al. 2019).
Fig 3.
RT-qPCR analysis of COG gene expression in COG-OE and COG-RNAi transgenic roots.
The COG transgenic roots are a. COG1-2 (Glyma.20G188500), b. COG2-2 (Glyma.05G047300), c. COG3-1 (Glyma.13G114900), d. COG4-2 (Glyma.03G261100), e. COG5-1 (Glyma.14G029500), f. COG6-1 (Glyma.01G154500), g. COG7-2 (Glyma.12G013000) and h. COG8-1 (Glyma.16G120600) in comparison to the appropriate pRAP15 and pRAP17 controls. The control gene is RPS21 (Glyma.15G147700), Lawaju et al. 2020 [17]. The 2-ΔΔCT method has been used to determine the relative change in COG gene expression (the RT-qPCR target) caused by the COG-OE or COG-RNAi genetic engineering event as compared to the control (Livak and Schmittgen 2002). *Statistically significant, Student’s t-test p < 0.05.
Fig 4.
Relative transcript abundance of COG genes in MAPK-overexpressing roots.
a. COG1-1 analyzed by RNA seq, b. COG1-2 RNA analyzed by RT-qPCR, c. COG2-2 analyzed by RNA seq, d. COG2-2 analyzed by RT-qPCR, e. COG3-1 analyzed by RNA seq, f. COG3-1 analyzed by RT-qPCR, g. COG4-2 analyzed by RNA seq. h. COG4-2 analyzed by RT-qPCR. i. COG5-1 analyzed by RNA seq, j. COG5-1 analyzed by RT-qPCR, k. COG6-1 analyzed by RNA seq, l. COG6-1 analyzed by RT-qPCR, m. COG7-2-b analyzed by RNA seq, n. COG7-2-b analyzed by RT-qPCR, o. COG8-1 analyzed by RNA seq, p. COG8-2 analyzed by RT-qPCR. Single replicate RNA seq analyses have been performed of RNA isolated from MAPK overexpressing roots. These results have been confirmed by RT-qPCR. The MAPK overexpressing roots include MAPK2 (Glyma.06G029700), MAPK3-1 (Glyma.U021800), MAPK 3–2 (Glyma.12G073000), MAPK 4–1 (Glyma.07G066800), MAPK 5–3 (Glyma.08G017400), MAPK6-2 (Glyma.07G206200), MAPK 13–1 (Glyma.12G073700), MAPK16-4 (Glyma.07G255400) and MAPK20-2 (Glyma.14G028100) and the appropriate pRAP15 control. The RNA seq data is shown as normalized log2(fold change) with a p-value cutoff of < 0.05. The RT-qPCR data is shown after employing the 2-ΔΔCT method of Livak and Schmittgen (2002) to determine the relative change in COG gene expression caused by the MAPK-OE genetic engineering event as compared to the control. *Statistically significant and meeting the 1.5 fold induced criteria, Student’s t-test p < 0.05. **Statistically significant and meeting the 1.5 fold induced criteria in RNA seq and RT-qPCR analyses.
Fig 5.
The COG complex functions in defense. B. A pathogen effector alters the functionality of the COG complex, leading to susceptibility. C. The COG complex composition becomes altered with a splice variant (COG7-2-b*, Glyma.12G013000.2) which alters the ability of the pathogen effector to bind, restoring the ability of the COG complex to function in defense, leading to a resistant reaction. VM, vesicle membrane; GM, Golgi membrane. The position of the COG proteins in relation to the Golgi and vesicle membranes does not imply specific interactions.