Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)

Table 1

Basic genomic information about gene families TaDCL, TaAGO, and TaRDR and properties of the encoded proteins in wheat (T. aestivum).

Gene no.	Gene name	Accession number	Genomic location	Gene length (bp)	Protein				Type
					No. of introns	Molecular weight (D.a)	Protein length (a.a.)	pI
DCL
1	TaDCL1a	Traes_4BL_B3A1B8342.2	ta_iwgsc_4bl_v1_6994694:2688..13103	10416	18	195505.38	1756	6.43	DCL1
2	TaDCL1b	Traes_5AL_72A7552B9.2	ta_iwgsc_5al_v1_2752914:2855..12171	9317	17	187281.30	1674	6.19	DCL1
3	TaDCL3a	Traes_1AL_E7144546E.1	ta_iwgsc_1al_v2_3918617:7862..20042	12181	25	184016.48	1627	6.39	DCL3
4	TaDCL3b	Traes_1DL_C646B6990.1	ta_iwgsc_1dl_v1_2224660:33..11929	11897	22	169269.68	1494	6.46	DCL3
5	TaDCL3c	Traes_3AL_562D6614F.1	ta_iwgsc_3al_v1_4401047:3091..12058	8968	23	177350.72	1586	6.04	DCL3
6	TaDCL3d	Traes_3DL_2DC78B18A.1	ta_iwgsc_3dl_v1_6937552:192..8538	8347	23	177414.90	1586	6.06	DCL3
7	TaDCL4	Traes_2DL_E96DCDCB4.2	ta_iwgsc_2dl_v1_9883052:5868..20610	14743	18	157968.69	1392	5.92	DCL4
AGO
1	TaAGO1a	Traes_2AL_2512A7F91.1	ta_iwgsc_2al_v1_6428016:16577..22920	6344	21	123940.53	1117	9.48	AGO1
2	TaAGO1b	Traes_2BL_93099ACF4.1	ta_iwgsc_6al_v1_5742333:938..12517	11580	16	72763.47	645	9.21	AGO1
3	TaAGO1c	Traes_6AL_616161AAB.1	ta_iwgsc_6al_v1_5742333:938..12517	11580	21	108532.11	978	9.48	AGO1
4	TaAGO1d	Traes_6DL_58620B158.2	ta_iwgsc_6dl_v1_3210843:3..6281	6279	21	101586.27	910	9.35	AGO1
5	TaAGO1e	Traes_7DL_C255A109C.1	ta_iwgsc_7dl_v1_3396214:4962..9930	4969	14	77484.04	721	9.22	AGO1
6	TaAGO1f	Traes_6BL_9CFA54D4A.1	ta_iwgsc_6bl_v1_4398549:8497..16669	8173	21	119364.74	1068	9.56	AGO1
7	TaAGO1g	Traes_6AL_317133B3F.2	ta_iwgsc_6al_v1_5770608:7589..20031	12443	22	120920.18	1085	9.60	AGO1
8	TaAGO1h	Traes_6DL_804FB7F75.1	ta_iwgsc_6dl_v1_3318900:4215..12555	8341	21	119065.35	1067	9.58	AGO1
9	TaAGO1i	Traes_7AS_56569A5AC.2	ta_iwgsc_7as_v1_4062808:1122..8394	7273	21	133941.63	1210	9.41	AGO1
10	TaAGO1j	Traes_7DS_4D01B6175.1	ta_iwgsc_7ds_v1_3925271:1281..7139	5859	21	97926.28	868	9.31	AGO1
11	TaAGO1k	Traes_4AL_A118C6C84.2	ta_iwgsc_4al_v2_7127490:1302..7644	6343	21	131032.87	1189	9.51	AGO1
12	TaAGO2a	Traes_2AL_DFE4C65F6.2	ta_iwgsc_2al_v1_6435863:9..4673	4665	2	104716.17	952	9.23	AGO2
13	TaAGO2b	Traes_2BL_7713B3533.2	ta_iwgsc_2bl_v1_8046272:2..4842	4841	2	94598.13	845	9.17	AGO2
14	TaAGO3	Traes_2DL_A77212060.2	ta_iwgsc_2dl_v1_9902460:2552..5785	3234	2	95781.21	849	8.54	AGO3
15	TaAGO4a	Traes_3AS_8EE711E2C.2	ta_iwgsc_3as_v1_3376626:7020..14138	7119	21	111230.93	999	8.88	AGO4
16	TaAGO4b	Traes_3DS_57EA31670.1	ta_iwgsc_3ds_v1_2601767:2..5053	5052	17	88926.36	799	9.22	AGO4
17	TaAGO4c	Traes_3B_F4E4667F8.1	ta_iwgsc_3b_v1_10588096:6226..11781	5556	20	99622.27	918	9.21	AGO4
18	TaAGO5a	Traes_2BS_8368F6B5D.1	ta_iwgsc_2bs_v1_5155056:10..6355	6346	21	91375.57	815	9.02	AGO4
19	TaAGO5b	Traes_2DS_4CC8FD7E3.1	ta_iwgsc_2ds_v1_5380297:2..6639	6638	21	94300.29	838	9.10	AGO5
20	TaAGO5c	Traes_5BL_F505BF164.1	ta_iwgsc_5bl_v1_10819703:15714..21283	5570	19	82474.57	732	8.95	AGO5
21	TaAGO5d	Traes_4AL_7CC35DF1D.2	ta_iwgsc_4al_v2_7146652:9555..15647	6093	21	98771.25	875	9.18	AGO5
22	TaAGO5e	Traes_4DS_88D2821C6.2	ta_iwgsc_4ds_v1_2318247:117..6407	6291	21	103082.25	916	9.22	AGO5
23	TaAGO5f	Traes_3AS_3F8424E4E.1	ta_iwgsc_3as_v1_1779497:2..5110	5109	20	93220.12	832	9.18	AGO5
24	TaAGO5g	Traes_3B_CA99AB66C.1	ta_iwgsc_3b_v1_9317732:662..5865	5204	20	94133.21	841	9.25	AGO5
25	TaAGO6a	Traes_1BL_05F7B7DFA.1	ta_iwgsc_1bl_v1_2609948:748..7252	6505	19	100043.38	893	6.99	AGO5
26	TaAGO6b	Traes_5AL_07EFD5712.1	ta_iwgsc_5al_v1_2801172:3925..11424	7500	21	98228.56	883	9.31	AGO6
27	TaAGO6c	Traes_5DL_672EE3605.1	ta_iwgsc_5dl_v1_4504514:5254..15341	10088	21	98062.91	882	9.31	AGO6
28	TaAGO6d	Traes_5BL_F611D65E0.1	ta_iwgsc_5bl_v1_10861763:7394..17699	10306	21	98241.09	883	9.30	AGO6
29	TaAGO6e	Traes_7AL_D88450A3C.2	ta_iwgsc_7al_v1_944917:567..5236	4670	17	86268.90	768	9.09	AGO6
30	TaAGO7a	Traes_2AL_3F3117458.1	ta_iwgsc_2al_v1_6334464:10651..14850	4200	2	105787.59	934	9.23	AGO7
31	TaAGO7b	Traes_2BL_24111235C.1	ta_iwgsc_2bl_v1_7955795:2637..7172	4536	2	115033.19	1023	9.33	AGO7
32	TaAGO8	Traes_7AL_1BAB53DCE.1	ta_iwgsc_7al_v1_4478819:3359..8183	4825	21	101590.86	901	9.11	AGO8
33	TaAGO9a	Traes_1AL_095416BC0.1	ta_iwgsc_1al_v2_3876661:1149..9699	8551	20	102455.28	925	9.09	AGO9
34	TaAGO9b	Traes_1BL_7C037D478.2	ta_iwgsc_1bl_v1_3899789:1061..10207	9147	21	102872.66	927	9.06	AGO9
35	TaAGO9c	Traes_1DL_64B330BBB.2	ta_iwgsc_1dl_v1_2275968:1227..11215	9989	21	102361.16	922	9.06	AGO9
36	TaAGO10a	Traes_6AS_FBB2AFAAB.1	ta_iwgsc_6as_v1_4364847:5932..12979	7048	20	105777.22	948	9.37	AGO10
37	TaAGO10b	Traes_6DS_9DD64BD48.1	ta_iwgsc_6ds_v1_2082993:2072..10005	7934	20	99080.09	883	9.95	AGO10
38	TaAGO10c	Traes_7AL_96766587F.2	ta_iwgsc_7al_v1_4543530:3452..7823	4372	15	65968.92	583	8.88	AGO10
39.	TaAGO10d	Traes_7DL_C538856D4.1	ta_iwgsc_7dl_v1_3364674:1..5438	5438	18	74927.28	664	8.95	AGO10
RDR
1	TaRDR1a	Traes_6DL_4B89E8742.2	ta_iwgsc_6dl_v1_3272251:691..6878	6188	3	127488.70	1120	6.98	RDR1
2	TaRDR1b	Traes_6BL_78BEF51DD.1	ta_iwgsc_6bl_v1_4353480:4946..8011	3066	2	82713.43	727	6.82	RDR1
3	TaRDR1c	Traes_6AL_393C6B853.1	ta_iwgsc_6al_v1_5823227:4526..9827	5302	3	127483.82	1119	7.15	RDR1
4	TaRDR1d	Traes_6BL_0A9D15EDC.2	ta_iwgsc_6bl_v1_4254864:3..1709	1707	1	54258.16	484	8.42	RDR1
5	TaRDR1e	Traes_6BL_0BB5C493D.1	ta_iwgsc_6bl_v1_4369818:3771..6377	2607	2	38289.35	333	5.40	RDR1
6	TaRDR1f	Traes_6AL_13BC97E04.1	ta_iwgsc_6al_v1_5769298:833..7192	6360	3	127303.48	1116	8.53	RDR1
7	TaRDR1g	Traes_6BL_DF680C2AF.1	ta_iwgsc_6bl_v1_4369819:1195..5786	4592	4	108562.11	947	7.34	RDR1
8	TaRDR2a	Traes_2DL_6DB81005E.1	ta_iwgsc_2dl_v1_9891666:1..7150	7150	3	82516.60	732	6.38	RDR2
9	TaRDR2b	Traes_4AS_8D6311711.1	ta_iwgsc_4as_v2_5940771:10843..26735	15893	4	126947.12	1127	6.60	RDR2
10	TaRDR2c	Traes_4DL_2E9CE89D9.2	ta_iwgsc_4dl_v3_14391157:7408..18499	11092	4	130417.41	1156	8.15	RDR2
11	TaRDR2d	Traes_4DL_A54C80661.1	ta_iwgsc_4dl_v3_14383226:1730..7149	5420	2	97124.16	869	6.82	RDR2
12	TaRDR3	Traes_7BL_8CEC8F99B.2	ta_iwgsc_7bl_v1_6687438:7..10355	10349	13	70361.58	616	6.20	RDR3
13	TaRDR4	Traes_3AS_F27BB108C.2	ta_iwgsc_3as_v1_3345716:2930..10167	7238	6	50505.60	436	5.75	RDR4
14	TaRDR5	Traes_3B_2C6DB84FB.2	ta_iwgsc_3b_v1_10500163:2098..12737	10640	11	63011.89	560	6.84	RDR5
15	TaRDR6a	Traes_3B_DC77B5E89.1	ta_iwgsc_3b_v1_10414255:3..4337	4335	1	104445.56	923	7.29	RDR6
16	TaRDR6b	Traes_3DL_F32B49981.1	ta_iwgsc_3dl_v1_6945798:1..3009	3009	1	60535.30	543	6.71	RDR6

Genomic info such as gene names, accession number, genomic/chromosomal location, genome length, and protein length was collected from the Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html), and the molecular weight and pI values were predicted by the ExPASy ComputepI/Mwtool (http://au.expasy.org/tools /pi_tool.html). Molecular weights are in Daltons and “aa” means amino acid.