Genome-wide Identification and Expression Analysis of the RNAi-related Gene Families in Setaria viridis

doi:10.13560/j.cnki.biotech.bull.1985.2022-0478

Abstract

Abstract:

RNAi pathway is a derived pathway of RdDM pathway, proteins AGOs, DCLs and RDRs of which play important roles in plant growth and development and in responses to abiotic/biotic stresses. In order to study the sequence and structural characteristics of these three main proteins of the RNAi pathway in Setaria viridis, we identified 13 AGO genes, seven DCL genes and four RDR genes in S. viridis by comparative genomics. Further we predicted the protein subcellular localization, phylogenetic relationship and conserved domain of these proteins. Meanwhile, the transcriptome data were used to analyze the expression patterns of three types of genes families in different organs in 16 different growth stages and different growth conditions of S. viridis. Protein conserved domain analysis revealed that SvDCL3b and SvRDR3 were lack of important domains. Transcriptome analysis showed that SvAGO1b, SvDCL1a and SvRDR1 were highly expressed in each family, which might play a major role in the RNAi pathway, and the expression patterns of homologous genes of S. viridis and S. italica were basically the same. In conclusion, this study provides a preliminary theoretical basis for understanding the functions and roles of the three main genes of the RNAi pathway in regulating the epigenetic modification of S. viridis, and provides a reference for the molecular mechanism of domestication between S. viridis and S. italica.

Key words: RNAi, gene family identification, protein domain, transcriptome, Setaria viridis

LUO Hao-tian, WANG Long, WANG Yu-qian, WANG Yue, LI Jia-zhen, YANG Meng-ke, ZHANG Jie, DENG Xin, WANG Hong-yan. Genome-wide Identification and Expression Analysis of the RNAi-related Gene Families in Setaria viridis[J]. Biotechnology Bulletin, 2023, 39(1): 175-186.

Figures/Tables 8

References 33

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S. viridis phytozome gene ID	S. viridis gene name	S. viridis phytozome sequence length/aa	S. italica phytozome gene ID（var. Yugu1）	S. italica gene name	S. italica phytozome sequence length/aa	Identity/%
Sevir.9G565900.2	SvDCL1a	1 933	Seita.9G562200.1	SiDCL1a	1 933	99
Sevir.4G119200.1	SvDCL1b	313	Seita.4G153000.1	SiDCL1b	313	100
Sevir.3G331300.1	SvDCL1c	375	Seita.3G295600.1	SiDCL1c	375	99
Sevir.9G177900.1	SvDCL2	1 562	Seita.9G179200.1	SiDCL2	1 404	99
Sevir.5G427800.1	SvDCL3a	1 662	Seita.5G422300.1	SiDCL3a	1 662	99
Sevir.9G214200.2	SvDCL3b	1 493	Seita.9G215300.1	SiDCL3b	1 626	95
Sevir.7G171000.1	SvSHO1	1 632	Seita.7G162200.1	SiSHO1	1 632	99
Sevir.7G213000.1	SvAGO1b	1 146	Seita.7G201100.1	SiAGO1b	1 104	99
Sevir.1G385400.1	SvAGO1c	1 023	Seita.1G378700.1	SiAGO1c	1 023	99
Sevir.4G301000.1	SvAGO1d	1 050	Seita.4G288700.1	SiAGO1d	1 050	99
Sevir.7G248200.1	SvAGO2	1 024	Seita.7G236800.1	SiAGO2	1 024	99
Sevir.5G040900.1	SvAGO4a	902	Seita.5G043300.1	SiAGO4a	902	99
Sevir.3G120100.1	SvAGO4b	910	Seita.3G117800.1	SiAGO4b	910	99
Sevir.9G051150.1	SvMEL1	1 005	Seita.9G052000.1	SiMEL1	1 005	99
Sevir.9G137300.2	SvAGO12	765	Seita.9G138800.1	SiAGO12	1 088	99
Sevir.2G069400.2	SvAGO14	764	Seita.2G066500.1	SiAGO14	1 041	100
Sevir.2G154500.1	SvAGO16	886	Seita.2G148000.1	SiAGO16	910	100
Sevir.2G321900.2	SvAGO18	779	Seita.2G310800.1	SiAGO18	954	99
Sevir.9G365300.2	SvSHL4	881	Seita.9G359200.1	SiSHL4	1 030	99
Sevir.4G237200.2	SvPNH1	965	Seita.4G225900.3	SiPNH1	965	100
Sevir.1G318100.1	SvRDR1	1 120	Seita.1G312200.1	SiRDR1	1 123	99
Sevir.7G137100.1	SvRDR2	1 130	Seita.7G128700.1	SiRDR2	1 130	100
Sevir.7G003600.2	SvRDR3	616	Seita.7G020600.1	SiRDR3	1 150	99
Sevir.5G186200.1	SvSHL2	1 211	Seita.5G184800.1	SiSHL2	1 211	99

S. viridis phytozome gene ID	S. viridis gene name	S. viridis phytozome sequence length/aa	S. italica phytozome gene ID（var. Yugu1）	S. italica gene name	S. italica phytozome sequence length/aa	Identity/%
Sevir.9G565900.2	SvDCL1a	1 933	Seita.9G562200.1	SiDCL1a	1 933	99
Sevir.4G119200.1	SvDCL1b	313	Seita.4G153000.1	SiDCL1b	313	100
Sevir.3G331300.1	SvDCL1c	375	Seita.3G295600.1	SiDCL1c	375	99
Sevir.9G177900.1	SvDCL2	1 562	Seita.9G179200.1	SiDCL2	1 404	99
Sevir.5G427800.1	SvDCL3a	1 662	Seita.5G422300.1	SiDCL3a	1 662	99
Sevir.9G214200.2	SvDCL3b	1 493	Seita.9G215300.1	SiDCL3b	1 626	95
Sevir.7G171000.1	SvSHO1	1 632	Seita.7G162200.1	SiSHO1	1 632	99
Sevir.7G213000.1	SvAGO1b	1 146	Seita.7G201100.1	SiAGO1b	1 104	99
Sevir.1G385400.1	SvAGO1c	1 023	Seita.1G378700.1	SiAGO1c	1 023	99
Sevir.4G301000.1	SvAGO1d	1 050	Seita.4G288700.1	SiAGO1d	1 050	99
Sevir.7G248200.1	SvAGO2	1 024	Seita.7G236800.1	SiAGO2	1 024	99
Sevir.5G040900.1	SvAGO4a	902	Seita.5G043300.1	SiAGO4a	902	99
Sevir.3G120100.1	SvAGO4b	910	Seita.3G117800.1	SiAGO4b	910	99
Sevir.9G051150.1	SvMEL1	1 005	Seita.9G052000.1	SiMEL1	1 005	99
Sevir.9G137300.2	SvAGO12	765	Seita.9G138800.1	SiAGO12	1 088	99
Sevir.2G069400.2	SvAGO14	764	Seita.2G066500.1	SiAGO14	1 041	100
Sevir.2G154500.1	SvAGO16	886	Seita.2G148000.1	SiAGO16	910	100
Sevir.2G321900.2	SvAGO18	779	Seita.2G310800.1	SiAGO18	954	99
Sevir.9G365300.2	SvSHL4	881	Seita.9G359200.1	SiSHL4	1 030	99
Sevir.4G237200.2	SvPNH1	965	Seita.4G225900.3	SiPNH1	965	100
Sevir.1G318100.1	SvRDR1	1 120	Seita.1G312200.1	SiRDR1	1 123	99
Sevir.7G137100.1	SvRDR2	1 130	Seita.7G128700.1	SiRDR2	1 130	100
Sevir.7G003600.2	SvRDR3	616	Seita.7G020600.1	SiRDR3	1 150	99
Sevir.5G186200.1	SvSHL2	1 211	Seita.5G184800.1	SiSHL2	1 211	99

Name	Number of amino acids	Molecular weig Mw/Da	Theore- tical pI	Number of nega- tive amino acids	Number of posi- tive amino acids	Instability index	Aliphatic index	Grand average of hydropathicity	Subcellular localization
SvDCL1a	1 933	216 220.21	6.38	258	241	44.68	82.32	-0.401	Nucleus
SvDCL1b	313	35 044.76	5.01	52	36	38.74	82.88	-0.396	Nucleus
SvDCL1c	375	41 215.67	8.91	43	49	29.3	92.85	-0.186	Nucleus
SvDCL2	1 562	174 660.19	8.16	171	179	48.64	92.11	-0.169	Nucleus
SvDCL3a	1 662	185 841.70	6.01	213	187	44.64	91.94	-0.243	Nucleus
SvDCL3b	1 493	168 634.83	6	183	158	45.1	95.37	-0.142	Extracellular space
SvSHO1	1 632	184 872.59	6.33	210	194	44.42	90.29	-0.229	Nucleus
SvAGO1b	1 146	127 072.12	9.41	102	135	49.38	74.15	-0.475	Extracellular space
SvAGO1c	1 023	113 773.50	9.55	101	136	52.31	77.34	-0.5	Nucleus
SvAGO1d	1 050	116 775.50	9.24	105	130	50.52	74.78	-0.464	Nucleus
SvAGO2	1 024	110 757.88	9.31	98	129	38.85	75.78	-0.419	Nucleus
SvAGO4a	902	100 987.60	9.15	99	121	48.49	78.65	-0.429	Nucleus
SvAGO4b	910	101 572.16	9.02	99	117	48.16	79.03	-0.398	Nucleus
SvMEL1	1 005	111 633.67	9.18	104	128	50.36	79.68	-0.364	Chloroplast thylakoid lumen
SvAGO12	765	85 951.54	9.02	76	95	41.32	84.09	-0.336	Nucleus
SvAGO14	764	86 241.92	8.9	74	89	49.64	81.77	-0.293	Nucleus
SvAGO16	886	99 036.16	9.26	92	118	42.69	86.86	-0.296	Nucleus
SvAGO18	779	87 496.55	9.19	86	109	40.43	89.33	-0.338	Nucleus
SvSHL4	881	99 741.90	9.24	92	120	40.43	83.63	-0.366	Nucleus
SvPNH1	965	107 674.01	9.34	94	127	48.09	83.07	-0.356	Nucleus
SvRDR1	1 120	127 951.65	7.72	131	133	39.69	86.88	-0.247	Nucleus
SvRDR2	1 130	126 334.56	6.9	146	143	43.53	85.42	-0.223	Chloroplast thylakoid membrane
SvRDR3	616	69 258.84	6.54	77	73	52.21	77.4	-0.428	Nucleus
SvSHL2	1 211	136 712.9	6.48	156	149	41.81	79.41	-0.334	Nucleus

Name	Number of amino acids	Molecular weig Mw/Da	Theore- tical pI	Number of nega- tive amino acids	Number of posi- tive amino acids	Instability index	Aliphatic index	Grand average of hydropathicity	Subcellular localization
SvDCL1a	1 933	216 220.21	6.38	258	241	44.68	82.32	-0.401	Nucleus
SvDCL1b	313	35 044.76	5.01	52	36	38.74	82.88	-0.396	Nucleus
SvDCL1c	375	41 215.67	8.91	43	49	29.3	92.85	-0.186	Nucleus
SvDCL2	1 562	174 660.19	8.16	171	179	48.64	92.11	-0.169	Nucleus
SvDCL3a	1 662	185 841.70	6.01	213	187	44.64	91.94	-0.243	Nucleus
SvDCL3b	1 493	168 634.83	6	183	158	45.1	95.37	-0.142	Extracellular space
SvSHO1	1 632	184 872.59	6.33	210	194	44.42	90.29	-0.229	Nucleus
SvAGO1b	1 146	127 072.12	9.41	102	135	49.38	74.15	-0.475	Extracellular space
SvAGO1c	1 023	113 773.50	9.55	101	136	52.31	77.34	-0.5	Nucleus
SvAGO1d	1 050	116 775.50	9.24	105	130	50.52	74.78	-0.464	Nucleus
SvAGO2	1 024	110 757.88	9.31	98	129	38.85	75.78	-0.419	Nucleus
SvAGO4a	902	100 987.60	9.15	99	121	48.49	78.65	-0.429	Nucleus
SvAGO4b	910	101 572.16	9.02	99	117	48.16	79.03	-0.398	Nucleus
SvMEL1	1 005	111 633.67	9.18	104	128	50.36	79.68	-0.364	Chloroplast thylakoid lumen
SvAGO12	765	85 951.54	9.02	76	95	41.32	84.09	-0.336	Nucleus
SvAGO14	764	86 241.92	8.9	74	89	49.64	81.77	-0.293	Nucleus
SvAGO16	886	99 036.16	9.26	92	118	42.69	86.86	-0.296	Nucleus
SvAGO18	779	87 496.55	9.19	86	109	40.43	89.33	-0.338	Nucleus
SvSHL4	881	99 741.90	9.24	92	120	40.43	83.63	-0.366	Nucleus
SvPNH1	965	107 674.01	9.34	94	127	48.09	83.07	-0.356	Nucleus
SvRDR1	1 120	127 951.65	7.72	131	133	39.69	86.88	-0.247	Nucleus
SvRDR2	1 130	126 334.56	6.9	146	143	43.53	85.42	-0.223	Chloroplast thylakoid membrane
SvRDR3	616	69 258.84	6.54	77	73	52.21	77.4	-0.428	Nucleus
SvSHL2	1 211	136 712.9	6.48	156	149	41.81	79.41	-0.334	Nucleus

S. viridis Seq	S. italica Seq	Ka	Ks	Ka/Ks
SvDCL1a	SiDCL1a	4.50E-04	0.007448	0.060448
SvDCL2	SiDCL2	0.007684	0.016635	0.461898
SvDCL3a	SiDCL3a	0.001735	0.002233	0.776912
SvDCL3b	SiDCL3b	0.003205	0.008756	0.36609
SvSHO1	SiSHO1	0.001317	0.003678	0.358024
SvDCL1c	SiDCL1c	0.001188	0.003628	0.327395
SvDCL1b	SiDCL1b	0	0	1
SvAGO1b	SiAGO1b	0.003265	0.002469	1.32227
SvAGO1c	SiAGO1c	4.32E-04	0.004014	0.1077
SvAGO1d	SiAGO1d	0.002126	0.009241	0.230094
SvAGO2	SiAGO2	0.002176	0.005251	0.414369
SvAGO4a	SiAGO4a	0.001443	0.014678	0.098316
SvAGO4b	SiAGO4b	0.004078	0.008723	0.467525
SvMEL1	SiMEL1	0.001322	0.008187	0.161428
SvAGO14	SiAGO14	0	0.003712	0
SvAGO16	SiAGO16	0	0	1
SvAGO18	SiAGO18	0.002238	0.007426	0.301434
SvSHL4	SiSHL4	4.25E-04	0.004131	0.102776
SvPNH1	SiPNH1	0	0	1
SvAGO12	SiAGO12	0.001719	0.013044	0.131752
SvSHL2	SiSHL2	3.62E-04	0.001162	0.311114
SvRDR2	SiRDR2	0	0.001233	0
SvRDR1	SiRDR1	0.003106	0.005191	0.598413
SvRDR3	SiRDR3	0.021549	0.035874	0.600701