TALome and phenotypic analysis of Pakistani Xanthomonas oryzae pv. oryzae population revealed novel virulent TALEs contributing to bacterial blight of rice

Table 1 Transcriptional activator-like effector (TALE) genotypes of Xanthomonas oryzae pv. oryzae strains collected from different rice-growing regions of Pakistan

Genotypes	Strains names	Total strains	Detected putative tale fragments	Total tale fragments
G1	P-10, P-11, P-31, P-23, P-24, P-26, P-28, P-29, P-20, P-30, P-38, P-8, P-9, P-10, P-11, P-12, P-25, P-5, P-6, P-7, P-22, P-17, P-25, P-28	24	D1, D2, E1, E2, F, H, I, L1, L2, L3, L4, M, N, O1, O2, Q	16
G2	P-14, P-19	2	A, D1, D2, E1, E2, F, H, I, L1, L2, L3, L4, M, N, O1, O2, Q	17
G3	KP-3, KP-8, KP-9, KP-11, KP-16, KP-23, KP-29, KP-31, BG-1, BG-2, BG-5, BG-22, BN-6, LD-67, LD-35, LD-51, BN-7, BN-10, BN-13, BN-17, BN-18, BN-25, BG-25, BG-27, BG-32, BG-39, LD-3, P-17, P-32, LD-24, LD-31, LD-33, LD-36, LD-41, LD-46, LD-61, LD-71, LD-55, BN-12, BG-24, LD-2, KP-1, KP-2, KP-17, KP-34, LD-21, BG-8, LD-17, LD-20, LD-22, LD-42	51	D1, D2, E1, E2, F, H, I, K, L1, L2, L3, L4, M, O1, O2, Q, R	17
G4	P-35, P-36, P-37, P-25(Old), P-4, P-13, KP-10, KP-12, KP-13, KP-14, KP-18, KP-20, KP-21, P-23(Old), KP-15, P-15, P-16	17	D1, D2, E1, E2, F, H, I, K, L1, L2, L3, L4, M, N, O1, O2, Q	17
G5	LD-13	1	D1, D2, E1, E2, F, G, H, K, L1, L2, L3, L4, M, O1, O2, Q, R	17
G6	P-27	1	D1, D2, E1, E2, F, H, J, K, L1, L2, L3, L4, N, O1, O2, Q, S	17
G7	P-18	1	B, D1, D2, E1, E2, F, H, I, L1, L2, L3, L4, M, N, O, P, Q1, Q2	18
G8	KP-22	1	D1, D2, E1, E2, F, I, J, K, L1, L2, L3, L4, M, O1, O2, Q1, Q2, R1, R2, T	20
G9	KP-24	1	D1, D2, E1, E2, F, I, J, K, L1, L2, L3, L4, M, N, O, P, Q1, Q2	18
G10	BG-3	1	D1, D2, E1, E2, F, I, J, K, L1, L2, L3, L4, O1, O2, Q1, Q2, R1, R2	18
G11	LD-5	1	C, D1, D2, E1, E2, F, I, J, K, L1, L2, L3, L4, M, O1, O2, Q1, Q2, R1, R2	20

Strain classification into a given genotype was determined based on the presence/absence of tale fragments (labeled A–T, as shown in Fig. 1). The number of strains, detected fragments, and the total number of tale fragments in each genotype are presented separately. Fragments displaying intense hybridization were considered two and four bands, considering the intensity, thickness, and comparison with the single available Pakistani Xoo strain PkXoo1 (TALEs = 18), which exhibited multiple fragments at the same position. Specifically, TALE fragments D = D1, D2; E = E1, E2; L = L1, L2, L3, L4 (common to all genotypes); O = O1, O2 (in G1–G6, G8, G10, G11); Q = Q1, Q2 (in G7–G11), and R = R1, R2 (in G8, G10, G11) demonstrated intense hybridization, and were considered multiple fragments. Unique TALE fragments are shown with bold fonts and the genotypes/strains containing novel major virulent TALE/s are highlighted italic font