Identification and Expression Analysis of ACA Gene Family in Lettuce

doi:10.7668/hbnxb.20195225

Abstract

Abstract:

As one of the subfamily members of Ca²⁺-ATPase,ACA exerts a vital role in sustaining the intracellular Ca²⁺ concentration equilibrium and modulating plant growth and development in response to abiotic stress.To acquire an in-depth comprehension of the function of the lettuce ACA gene family,bioinformatics methodologies were utilized to identify and dissect the members of the lettuce ACA gene family.The outcomes manifested that 17 ACA genes were identified in lettuce,denominated as LsACA1 to LsACA17;the LsACA genes were unevenly distributed across 8 chromosomes;the subcellular localization prediction results disclosed that all LsACA proteins were localized in the plasma membrane;the number of introns exhibited significant variation(0—32)among the members of the LsACA gene family,a total of 15 conserved domains of LsACA proteins were identified,with amino acids ranging from 21 to 50;the proportion of the secondary structure was alpha helix>random coil>extended strand>beta turn;based on phylogenetic analysis,LsACA proteins were categorized into 5 subfamilies,namely Group Ⅰ to Group Ⅴ;according to collinearity analysis,it was found that there were fragment duplications in 6 pairs of genes,the Ka/Ks of their collinear gene pairs were all less than 1,signifying that purifying selection was the preponderant force in evolution.The expression patterns of LsACA gene family members under different calcium ion concentrations were analyzed by qRT-PCR.The results showed that:compared with the control,the expression levels of 12 LsACA genes in the calcium-sensitive variety Baoshilü under low calcium treatment were extremely significantly downregulated,while the expression levels of 9 LsACA genes in the calcium-insensitive variety Yeluo were extremely significantly upregulated and the expression level of 1 LsACA gene was significantly upregulated.The ACA gene family members of lettuce were identified and analyzed,and the characteristics of the LsACA gene family members were revealed.

Key words: Lettuce, Gene family, LsACA, Calcium, Expression analysis

ZHANG Qinqin, HOU Guangguang, LI Chang, DAI Bowen, WANG Xiaofang, XIE Ziwei, FAN Mi, WU Xiaolei, GAO Hongbo, LI Jingrui. Identification and Expression Analysis of ACA Gene Family in Lettuce[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(1): 63-73. doi: 10.7668/hbnxb.20195225.

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Figures/Tables 13

References 29

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基因名称 Gene name	上游引物(5'—3') Forward primer(5'—3')	下游引物(5'—3') Reverse primer(5'—3')
LsACA2	CTGTGCTTGGGATACCTGAT	GAAGAATAGCCACCCAGTGA
LsACA3	CCCTCCAAGACATGACTCTC	ACAACCAGCAAAATACTCGC
LsACA4	GTTGGTAGAGAAGATGGGGG	GCGGACAATAACACTCATCG
LsACA5	GGTGAAGACTTGTTTGGACG	CGCAGTCAAAATCCCACATT
LsACA6	TCAACAACATCGGGCATTTC	AATGCACAAACACCAAGGAC
LsACA7	CTTTGTTGGCTTAGCTGGAC	GCTGTGTTCTTGTTGTCTCC
LsACA8	ATGGGAATGGTGAAGTGGTT	GCAACAGATTCCTTCACACC
LsACA9	CTTAACGCGATTGTTGGTGT	AGCTCCACAATATCACCTGG
LsACA10	TCCAGCTTCTTTGGGTGAAT	TACAAGGAGCACCAACACTT
LsACA11	GGCTGTCCTATTCGTCTTGA	AATCCAACTGCTCAACATGC
LsACA12	GCTCTATTCACCAGAACCGA	GTCATGTTTTGAGGGTGAGC
LsACA13	TGACCGGGACTTTAACAACA	TATACCTTGCAGGAGCACAG
LsACA14	GAGGAATGTGTTTCAAGGGC	CGCTGCAATCGCTATACAAA
LsACA15	GCGGTGGTTTTGAGGATTAC	TCGACGTGAAGCATTGAGTA
LsACA17	TCAGTTCAGGGGTAAGGAGA	CAGTCATCCCAATGATCCCA
Actin	GGCAACTGGGATGACATGGAAA	GCACAGCCTGGATAGCAACATA

基因名称 Gene name	上游引物(5'—3') Forward primer(5'—3')	下游引物(5'—3') Reverse primer(5'—3')
LsACA2	CTGTGCTTGGGATACCTGAT	GAAGAATAGCCACCCAGTGA
LsACA3	CCCTCCAAGACATGACTCTC	ACAACCAGCAAAATACTCGC
LsACA4	GTTGGTAGAGAAGATGGGGG	GCGGACAATAACACTCATCG
LsACA5	GGTGAAGACTTGTTTGGACG	CGCAGTCAAAATCCCACATT
LsACA6	TCAACAACATCGGGCATTTC	AATGCACAAACACCAAGGAC
LsACA7	CTTTGTTGGCTTAGCTGGAC	GCTGTGTTCTTGTTGTCTCC
LsACA8	ATGGGAATGGTGAAGTGGTT	GCAACAGATTCCTTCACACC
LsACA9	CTTAACGCGATTGTTGGTGT	AGCTCCACAATATCACCTGG
LsACA10	TCCAGCTTCTTTGGGTGAAT	TACAAGGAGCACCAACACTT
LsACA11	GGCTGTCCTATTCGTCTTGA	AATCCAACTGCTCAACATGC
LsACA12	GCTCTATTCACCAGAACCGA	GTCATGTTTTGAGGGTGAGC
LsACA13	TGACCGGGACTTTAACAACA	TATACCTTGCAGGAGCACAG
LsACA14	GAGGAATGTGTTTCAAGGGC	CGCTGCAATCGCTATACAAA
LsACA15	GCGGTGGTTTTGAGGATTAC	TCGACGTGAAGCATTGAGTA
LsACA17	TCAGTTCAGGGGTAAGGAGA	CAGTCATCCCAATGATCCCA
Actin	GGCAACTGGGATGACATGGAAA	GCACAGCCTGGATAGCAACATA

基因 Gene	基因ID Gene ID	氨基酸数量/个 Number of amino acids	分子质量/ku Molecular weight	理论等电点 Theoretical pI	不稳定指数 Instability index	脂溶指数 Aliphatic index	总平均疏水指数 Grand average of hydropathicity (GRAVY)	跨膜结构域数目/个 Transmembrane domain number	亚细胞定位 (综合分值) Subcellular location (Subcellular score)
LsACA1	LSAT_3X86121	989	107.878 06	6.63	32.77	100.22	0.129	8	细胞质膜(13)
LsACA2	LSAT_9X76580	1 001	109.458 18	5.83	37.56	103.03	0.248	8	细胞质膜(9)
LsACA3	LSAT_4X160760	1 004	109.584 61	5.85	33.41	97.28	0.096	8	细胞质膜(11)
LsACA4	LSAT_7X2840	1 047	114.835 86	5.10	31.50	98.08	0.101	8	细胞质膜(10)
LsACA5	LSAT_1X99900	1 033	113.780 90	7.77	38.35	107.83	0.164	8	细胞质膜(9)
LsACA6	LSAT_2X83261	1 017	111.275 98	6.06	27.42	104.16	0.170	8	细胞质膜(11)
LsACA7	LSAT_5X167061	1 062	116.732 14	5.28	32.47	97.67	-0.017	8	细胞质膜(13)
LsACA8	LSAT_4X131720	1 016	111.690 48	5.73	31.56	103.20	0.134	6	细胞质膜(11)
LsACA9	LSAT_8X78840	1 062	116.111 30	5.30	31.85	98.63	0.008	9	细胞质膜(11)
LsACA10	LSAT_8X68280	1 084	118.382 97	6.86	37.91	103.39	0.085	7	细胞质膜(12)
LsACA11	LSAT_9X30940	1 029	112.414 67	6.07	34.85	105.10	0.178	8	细胞质膜(9)
LsACA12	LSAT_8X82040	1 033	113.538 22	5.80	34.84	104.06	0.152	10	细胞质膜(11)
LsACA13	LSAT_8X82100	876	94.966 48	5.11	33.10	102.11	0.243	6	细胞质膜(10)
LsACA14	LSAT_5X185301	975	107.469 65	7.17	28.76	101.16	0.067	8	细胞质膜(13)
LsACA15	LSAT_5X84040	1 090	118.986 08	5.98	36.86	101.23	0.040	6	细胞质膜(13)
LsACA16	LSAT_4X88560	1 041	114.542 72	5.99	40.37	101.11	0.028	8	细胞质膜(12)
LsACA17	LSAT_9X7821	1 011	111.947 81	6.41	34.20	101.87	0.086	8	细胞质膜(11)

基因 Gene	基因ID Gene ID	氨基酸数量/个 Number of amino acids	分子质量/ku Molecular weight	理论等电点 Theoretical pI	不稳定指数 Instability index	脂溶指数 Aliphatic index	总平均疏水指数 Grand average of hydropathicity (GRAVY)	跨膜结构域数目/个 Transmembrane domain number	亚细胞定位 (综合分值) Subcellular location (Subcellular score)
LsACA1	LSAT_3X86121	989	107.878 06	6.63	32.77	100.22	0.129	8	细胞质膜(13)
LsACA2	LSAT_9X76580	1 001	109.458 18	5.83	37.56	103.03	0.248	8	细胞质膜(9)
LsACA3	LSAT_4X160760	1 004	109.584 61	5.85	33.41	97.28	0.096	8	细胞质膜(11)
LsACA4	LSAT_7X2840	1 047	114.835 86	5.10	31.50	98.08	0.101	8	细胞质膜(10)
LsACA5	LSAT_1X99900	1 033	113.780 90	7.77	38.35	107.83	0.164	8	细胞质膜(9)
LsACA6	LSAT_2X83261	1 017	111.275 98	6.06	27.42	104.16	0.170	8	细胞质膜(11)
LsACA7	LSAT_5X167061	1 062	116.732 14	5.28	32.47	97.67	-0.017	8	细胞质膜(13)
LsACA8	LSAT_4X131720	1 016	111.690 48	5.73	31.56	103.20	0.134	6	细胞质膜(11)
LsACA9	LSAT_8X78840	1 062	116.111 30	5.30	31.85	98.63	0.008	9	细胞质膜(11)
LsACA10	LSAT_8X68280	1 084	118.382 97	6.86	37.91	103.39	0.085	7	细胞质膜(12)
LsACA11	LSAT_9X30940	1 029	112.414 67	6.07	34.85	105.10	0.178	8	细胞质膜(9)
LsACA12	LSAT_8X82040	1 033	113.538 22	5.80	34.84	104.06	0.152	10	细胞质膜(11)
LsACA13	LSAT_8X82100	876	94.966 48	5.11	33.10	102.11	0.243	6	细胞质膜(10)
LsACA14	LSAT_5X185301	975	107.469 65	7.17	28.76	101.16	0.067	8	细胞质膜(13)
LsACA15	LSAT_5X84040	1 090	118.986 08	5.98	36.86	101.23	0.040	6	细胞质膜(13)
LsACA16	LSAT_4X88560	1 041	114.542 72	5.99	40.37	101.11	0.028	8	细胞质膜(12)
LsACA17	LSAT_9X7821	1 011	111.947 81	6.41	34.20	101.87	0.086	8	细胞质膜(11)

基因 Gene	α-螺旋 Alpha helix	延伸链 Extended strand	无规则卷曲 Random coil	β-折叠 Beta turn
LsACA1	43.68	19.62	29.93	6.77
LsACA2	48.05	18.28	27.97	5.69
LsACA3	44.12	20.22	28.49	7.17
LsACA4	44.13	17.00	32.95	5.92
LsACA5	44.14	18.88	30.30	6.68
LsACA6	44.94	19.37	28.81	6.88
LsACA7	44.82	17.33	31.45	6.40
LsACA8	44.88	19.39	28.35	7.38
LsACA9	44.26	17.61	32.39	5.74
LsACA10	42.25	19.00	32.47	6.27
LsACA11	43.83	18.66	31.58	5.93
LsACA12	43.66	18.39	30.88	7.07
LsACA13	43.38	18.95	31.51	6.16
LsACA14	41.95	20.31	31.28	6.46
LsACA15	42.02	18.72	32.75	6.51
LsACA16	43.23	19.88	30.74	6.15
LsACA17	43.62	20.08	29.48	6.82

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