Identification and Evolutionary Analysis of Maize DUF1685 Gene Family

doi:10.3969/j.issn.1000-2561.2022.12.005

Abstract

Abstract:

A total of 211 DUF1685 gene family members in 16 monocotyledonous and dicotyledon and Selaginella moellendorffii were identified in this study. Analysis of protein physicochemical properties showed that the amino acid sequences of 211 DUF1685 genes ranged in length from 83 to 1071 aa, molecular weights from 9.2 to 116.3 kDa, and theoretical isoelectric points from 3.66 to 11.90. Phylogenetic evolution analysis showed that the DUF1685 gene family were divided into three subfamilies (Class I, Class II and Class III). The events of A1 and A2, B1 and B2 in the Class I and Class II subfamilies occurred after the differentiation of monocotyledonous plants, and A1 and B2 branches (members were all dicotyledonous genes) had gene expansion phenomenon. The results of conserved motifs and gene structure analysis showed that the conserved motifs among members of the same subfamily were similar. Most of the 211 DUF1685 family genes contained one intron, and a few genes contained two or more introns or no introns. Selection pressure analysis showed that the related loci of DUF1685 family genes were positively selected during the evolution process, which may be the reason for the functional changes of some genes. Collinearity analysis indicated that fragment duplication events may be a potential driver of DUF1685 gene amplification and evolution in the maize. The results of cis-element analysis in the gene promoter region showed that the promoter region of maize DUF1685 gene contained light-responsive elements, ABA and cis-acting elements related to abiotic stress. It was speculated that the genes may be involved in the response of maize to abiotic stress. Transcriptome data analysis revealed that the maize DUF1685 gene was associated with the growth and development of specific tissues (mature pollen). This study explored the function and evolution of the maize DUF1685 gene family in various aspects to provide a theoretical reference for the in-depth study of the biological function and evolutionary relationship of the maize DUF1685 gene in the future.

Key words: DUF1685 gene, gene identification, evolutionary analysis

CLC Number:

S513

LUO Xuan, LIN Zhengyu, CHEN Zhang, LEI Bo, LI Jie, QUAN Jinying, LIU Hailan. Identification and Evolutionary Analysis of Maize DUF1685 Gene Family[J]. Chinese Journal of Tropical Crops, 2022, 43(12): 2431-2442.

Figures/Tables 10

References 35

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类别 Categary	植物名称 Plant name	基因数量 Nmuber of gene
石松植物门	卷柏Selaginella moellendorffii	5
双子叶植物	拟南芥Arabidopsis thaliana	9
	甘蓝Brassica oleracea	12
	甘蓝型油菜Brassica napus	34
	白菜Brassica rapa	16
	萝卜Raphanus sativus	15
	芥菜型油菜Brassica juncea	33
	黑芥Brassica nigra	16
	棉花Gossypium raimondii	15
	大豆Glycine max	10
	苜蓿Medicago truncatula	6
单子叶植物	大麦Hordeum vulgare	5
	水稻Oryza sativa	5
	玉米Zea mays	7
	高粱Sorghum bicolor	6
	菠萝Ananas comosus	6
	柳枝稷Panicum virgatum	11

类别 Categary	植物名称 Plant name	基因数量 Nmuber of gene
石松植物门	卷柏Selaginella moellendorffii	5
双子叶植物	拟南芥Arabidopsis thaliana	9
	甘蓝Brassica oleracea	12
	甘蓝型油菜Brassica napus	34
	白菜Brassica rapa	16
	萝卜Raphanus sativus	15
	芥菜型油菜Brassica juncea	33
	黑芥Brassica nigra	16
	棉花Gossypium raimondii	15
	大豆Glycine max	10
	苜蓿Medicago truncatula	6
单子叶植物	大麦Hordeum vulgare	5
	水稻Oryza sativa	5
	玉米Zea mays	7
	高粱Sorghum bicolor	6
	菠萝Ananas comosus	6
	柳枝稷Panicum virgatum	11

亚家族 Subfamily	模型Model	dN/dS(ω)	参数估计 Estimates of parameters	正选择位点 Positively selected sites	似然比检验（P值） Likelihood ratio test (P value)
Class I （A1）	M0	0.2804	ω=0.280 40	None	2Δlnl (M0 vs M3)=758.85 (P<0.001) 2Δlnl (M1 vs M2)=10.87 (P<0.001) 2Δlnl (M7 vs M8)=19.41 (P<0.001)
	M1	0.6037	p₀=0.423 38 (p₁=0.576 62)	Not allowed
	M2	0.7078	p₀=0.416 87, p₁=0.489 10 (p₂= 0.094 02), ω₂=2.028 98	129L
	M3	0.4993	p₀=0.372 92, p₁=0.282 68 (p₂=0.344 40) ω₀=0.040 26, ω₁=0.368 83, ω₂=1.057 94	Many
	M7	0.4327	p=0.474 68, q=0.622 25	Not allowed
	M8	0.4830	p₀=0.773 06 (p₁=0.226 94) p=0.580 33, q=1.545 51, ω=1.205 03	129L
Class I （A2）	M0	0.2161	ω=0.216 10	None	2Δlnl (M0 vs M3)=356.15 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=18.76 (P<0.001)
	M1	0.5260	p₀=0.540 94 (p₁= 0.459 06)	Not allowed
	M2	0.5260	p₀=0.540 94, p₁=0.221 75 (p₂=0.237 31), ω₂=1.000 00	320 327
	M3	0.3339	p₀=0.194 86, p₁=0.409 50 (p₂=0.395 64) ω₀=0.013 19, ω₁=0.181 15, ω₂=0.650 04	—
	M7	0.3430	p=0.569 65, q=1.086 47	Not allowed
	M8	0.9463	p₀=0.911 31(p₁=0.088 69) p=0.644 37, q=1.553 61, ω=7.676 29	320 327
Class II （B1）	M0	0.2046	ω=0.204 60	None	2Δlnl (M0 vs M3)=309.57 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=15.26 (P<0.001)
	M1	0.4187	p₀=0.653 79 (p₁=0.346 21)	Not allowed
	M2	0.4187	p₀=0.653 79, p₁=0.284 11 (p₂=0.062 09), ω₂=1.000 00	—
	M3	0.3332	p₀=0.387 17, p₁=0.466 77 (p₂=0.146 07) ω₀=0.038 18, ω₁=0.299 61, ω₂=1.222 36	Many
	M7	0.2915	p=0.551 73, q=1.331 02	Not allowed
	M8	3.6758	p₀=0.969 96 (p₁=0.030 04) p=0.599 66, q=1.598 75, ω=113.620 63	338P
Class II （B2）	M0	0.1827	ω=0.182 70	None	2Δlnl (M0 vs M3)=298.50 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=0.00 (P=1.000)
	M1	0.3588	p₀=0.732 14 (p₁=0.267 86)	Not allowed
	M2	0.3588	p₀=0.732 14, p₁=0.0768 90 (p₂=0.190 97), ω₂=1.000 00	—
	M3	0.2149	p₀=0.325 22, p₁=0.374 94 (p₂=0.299 84)ω₀=0.009 03, ω₁=0.174 85, ω₂=0.488 29	—
	M7	0.2167	p=0.509 79, q=1.814 23	Not allowed
	M8	0.2167	p₀=0.999 99 (p₁=0.000 01) p=0.509 81, q=1.814 41, ω=1.216 11	—
Class III	M0	0.2882	ω=0.288 2	None	2Δlnl (M0 vs M3)=607.62 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=204.29 (P<0.001)
	M1	0.5642	p₀=0.526 87 (p₁=0.473 13)	Not allowed
	M2	0.5642	p₀=0.526 87, p₁=0.071 42 (p₂=0.401 70), ω₂=1.000 00	—
	M3	9.5791	p₀=0.307 06, p₁=0.473 78 (p₂=0.219 16) ω₀=0.111 37, ω₁=0.111 37, ω₂=42.538 39	Many
	M7	0.4731	p=0.778 83, q=0.866 74	Not allowed
	M8	9.3514	p₀=0.785 28 (p₁=0.214 72) p=1.066 73, q=1.901 71, ω= 42.241 90	141 Sites

亚家族 Subfamily	模型Model	dN/dS(ω)	参数估计 Estimates of parameters	正选择位点 Positively selected sites	似然比检验（P值） Likelihood ratio test (P value)
Class I （A1）	M0	0.2804	ω=0.280 40	None	2Δlnl (M0 vs M3)=758.85 (P<0.001) 2Δlnl (M1 vs M2)=10.87 (P<0.001) 2Δlnl (M7 vs M8)=19.41 (P<0.001)
	M1	0.6037	p₀=0.423 38 (p₁=0.576 62)	Not allowed
	M2	0.7078	p₀=0.416 87, p₁=0.489 10 (p₂= 0.094 02), ω₂=2.028 98	129L
	M3	0.4993	p₀=0.372 92, p₁=0.282 68 (p₂=0.344 40) ω₀=0.040 26, ω₁=0.368 83, ω₂=1.057 94	Many
	M7	0.4327	p=0.474 68, q=0.622 25	Not allowed
	M8	0.4830	p₀=0.773 06 (p₁=0.226 94) p=0.580 33, q=1.545 51, ω=1.205 03	129L
Class I （A2）	M0	0.2161	ω=0.216 10	None	2Δlnl (M0 vs M3)=356.15 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=18.76 (P<0.001)
	M1	0.5260	p₀=0.540 94 (p₁= 0.459 06)	Not allowed
	M2	0.5260	p₀=0.540 94, p₁=0.221 75 (p₂=0.237 31), ω₂=1.000 00	320 327
	M3	0.3339	p₀=0.194 86, p₁=0.409 50 (p₂=0.395 64) ω₀=0.013 19, ω₁=0.181 15, ω₂=0.650 04	—
	M7	0.3430	p=0.569 65, q=1.086 47	Not allowed
	M8	0.9463	p₀=0.911 31(p₁=0.088 69) p=0.644 37, q=1.553 61, ω=7.676 29	320 327
Class II （B1）	M0	0.2046	ω=0.204 60	None	2Δlnl (M0 vs M3)=309.57 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=15.26 (P<0.001)
	M1	0.4187	p₀=0.653 79 (p₁=0.346 21)	Not allowed
	M2	0.4187	p₀=0.653 79, p₁=0.284 11 (p₂=0.062 09), ω₂=1.000 00	—
	M3	0.3332	p₀=0.387 17, p₁=0.466 77 (p₂=0.146 07) ω₀=0.038 18, ω₁=0.299 61, ω₂=1.222 36	Many
	M7	0.2915	p=0.551 73, q=1.331 02	Not allowed
	M8	3.6758	p₀=0.969 96 (p₁=0.030 04) p=0.599 66, q=1.598 75, ω=113.620 63	338P
Class II （B2）	M0	0.1827	ω=0.182 70	None	2Δlnl (M0 vs M3)=298.50 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=0.00 (P=1.000)
	M1	0.3588	p₀=0.732 14 (p₁=0.267 86)	Not allowed
	M2	0.3588	p₀=0.732 14, p₁=0.0768 90 (p₂=0.190 97), ω₂=1.000 00	—
	M3	0.2149	p₀=0.325 22, p₁=0.374 94 (p₂=0.299 84)ω₀=0.009 03, ω₁=0.174 85, ω₂=0.488 29	—
	M7	0.2167	p=0.509 79, q=1.814 23	Not allowed
	M8	0.2167	p₀=0.999 99 (p₁=0.000 01) p=0.509 81, q=1.814 41, ω=1.216 11	—
Class III	M0	0.2882	ω=0.288 2	None	2Δlnl (M0 vs M3)=607.62 (P<0.001) 2Δlnl (M1 vs M2)=0.00 (P=1.000) 2Δlnl (M7 vs M8)=204.29 (P<0.001)
	M1	0.5642	p₀=0.526 87 (p₁=0.473 13)	Not allowed
	M2	0.5642	p₀=0.526 87, p₁=0.071 42 (p₂=0.401 70), ω₂=1.000 00	—
	M3	9.5791	p₀=0.307 06, p₁=0.473 78 (p₂=0.219 16) ω₀=0.111 37, ω₁=0.111 37, ω₂=42.538 39	Many
	M7	0.4731	p=0.778 83, q=0.866 74	Not allowed
	M8	9.3514	p₀=0.785 28 (p₁=0.214 72) p=1.066 73, q=1.901 71, ω= 42.241 90	141 Sites

顺式作用元件 Cis-acting element	数量/基因名称 Number/Gene name	注释 Note
ABRE	3/Zm00001d004209, 1/Zm00001d012154, 4/Zm00001d042503, 3/Zm00001d049091, 1/Zm00001d052162, 2/Zm00001d052162, 4/Zm00001d024004	ABA响应元件
TATA-box	17/Zm00001d004209, 35/Zm00001d012154, 16/Zm00001d042503, 30/Zm00001d049091, 1/Zm00001d052162, 62/Zm00001d052162, 64/Zm00001d024004	转录起始-30核心启动子元件
MYC	4/Zm00001d004209, 3/Zm00001d012154, 2/Zm00001d042503, 2/Zm00001d049091, 1/Zm00001d052162, 4/Zm00001d052162, 4/Zm00001d024004	干旱和ABA应答元件
G-box	5/Zm00001d004209, 3/Zm00001d012154, 4/Zm00001d042503, 7/Zm00001d049091, 2/Zm00001d052162, 3/Zm00001d052162, 7/Zm00001d024004	光响应元件
CAAT-box	24/Zm00001d004209, 28/Zm00001d012154, 28/Zm00001d042503, 18/Zm00001d049091, 1/Zm00001d052162, 36/Zm00001d052162, 33/Zm00001d024004	顺式作用元件
MYB	6/Zm00001d004209, 2/Zm00001d012154,6/Zm00001d042503, 2/Zm00001d049091, 1/Zm00001d052162, 5/Zm00001d052162, 2/Zm00001d024004	干旱和ABA应答元件
STRE	6/Zm00001d004209, 6/Zm00001d012154, 3/Zm00001d042503, 3/Zm00001d049091, 1/Zm00001d052162, 2/Zm00001d052162, 9/Zm00001d024004	热诱导元件