Identification of CAX gene family and expression profile analysis of response to abiotic stress in alfalfa

doi:10.11686/cyxb2021471

Abstract

Abstract:

Ca²⁺/H⁺ reverse transporter proteins （CAX） are an important group of transmembrane transporters， which plays important roles in regulating Ca²⁺ balance， resisting abiotic stresses and transporting heavy metal ions in plants. Using bioinformatics methods， we performed a genome-wide identification of CAX gene family occurrence in alfalfa. In this work， the physicochemical properties， structural characteristics， phylogenetic relationships， cis-acting elements and chromosome locations of CAX gene family members were analyzed. Fifteen MsCAX genes were identified and these were distributed on 15 alfalfa chromosomes with 22 pairs of segmental duplication events. Further analysis showed that they encoded 367-460 amino acids with isoelectric points ranging from pH 5.2 to 6.5. All of them were hydrophobic proteins. Phylogenetic analysis showed that MsCAXs were divided into two subfamilies， and members of the same subfamily had similar genetic structures， conserved motifs， and the number of transmembrane domains. The promoter region of MsCAXs contained the light， hormone and stress-responsive elements. The expression patterns of six MsCAXs genes in response to abiotic stress were analyzed by qRT-PCR. It was found that all six MsCAX genes were significantly down-regulated under drought and low temperature stress， and three MsCAX genes were up-regulated under salt and saline-alkali stress. These results indicate that MsCAX gene has different expression patterns under different abiotic stresses. The results provide a reference for further exploration of the functions of the MsCAX gene family.

Key words: alfalfa, CAX gene family, genome-wide gene identification, abiotic stress, gene expression

Guo-xiang ZHANG, Wei-leng GUO, Ming-yu BI, Li-shuang ZHANG, Dan WANG, Chang-hong GUO. Identification of CAX gene family and expression profile analysis of response to abiotic stress in alfalfa[J]. Acta Prataculturae Sinica, 2022, 31(12): 106-117.

Figures/Tables 10

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基因Gene	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
MsCAX1	TTGTTGTTGATGGCTGTAATGG	CAAGTTCTTCCTCCTCGTCAG
MsCAX2	GTTGTTGATGGCTGTAATGGG	CCTCGTCAGAGTTTTCACTTGTA
MsCAX3	TTGGGAAGTCCGTCTTATCTC	GACAACACTGATACCCATACCG
MsCAX11	GACAGAAAACAGGCAGATGTAAAT	AATGTCATACCCACCAACCA
MsCAX12	ATGAGGCAGAAGAAGAGGCT	GCGAAAATGATTGCTCCTG
MsCAX15	ATGTGCTTCGCTTAGGGTC	CATTAAGAAGTCCTCCAACTGTAG
MsGAPDH	ACGAGCGTTTCAGATG	ACCTCCGATCCAGACA

基因Gene	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
MsCAX1	TTGTTGTTGATGGCTGTAATGG	CAAGTTCTTCCTCCTCGTCAG
MsCAX2	GTTGTTGATGGCTGTAATGGG	CCTCGTCAGAGTTTTCACTTGTA
MsCAX3	TTGGGAAGTCCGTCTTATCTC	GACAACACTGATACCCATACCG
MsCAX11	GACAGAAAACAGGCAGATGTAAAT	AATGTCATACCCACCAACCA
MsCAX12	ATGAGGCAGAAGAAGAGGCT	GCGAAAATGATTGCTCCTG
MsCAX15	ATGTGCTTCGCTTAGGGTC	CATTAAGAAGTCCTCCAACTGTAG
MsGAPDH	ACGAGCGTTTCAGATG	ACCTCCGATCCAGACA

基因登录号 Gene ID	基因名 Gene name	氨基酸长度 Amino acid length （aa）	等电点 PI	分子量 Molecular weight （kDa）	不稳定指数 Instability index	疏水性指数 GRAVY	脂肪指数 Aliphatic index	跨膜结构数目 No. of transmembrane domains
MS.gene99860	MsCAX1	460	5.52	49.87385	44.42	0.516	104.72	11
MS.gene83511	MsCAX2	446	5.41	48.36603	44.32	0.544	105.81	11
MS.gene067498	MsCAX3	464	5.62	50.36244	44.47	0.511	104.44	11
MS.gene70485	MsCAX4	407	5.20	44.38009	37.15	0.562	120.69	9
MS.gene044358	MsCAX5	367	5.50	39.90768	34.51	0.483	120.84	8
MS.gene044315	MsCAX6	442	5.21	48.20153	34.66	0.570	117.08	9
MS.gene057847	MsCAX7	457	5.36	50.22957	29.72	0.524	116.56	10
MS.gene43800	MsCAX8	434	6.50	47.51891	31.02	0.609	121.98	10
MS.gene44897	MsCAX9	434	6.50	47.54693	30.85	0.608	121.98	10
MS.gene009878	MsCAX10	434	6.50	47.50088	31.46	0.615	122.88	10
MS.gene88788	MsCAX11	420	6.30	45.83903	28.84	0.656	126.98	10
MS.gene84200	MsCAX12	455	5.74	49.23152	37.33	0.580	123.25	11
MS.gene77339	MsCAX13	455	5.74	49.23355	38.06	0.582	122.62	11
MS.gene92638	MsCAX14	455	5.74	49.23355	38.06	0.582	122.62	11
MS.gene78431	MsCAX15	455	5.74	49.22955	36.91	0.586	123.47	11

基因登录号 Gene ID	基因名 Gene name	氨基酸长度 Amino acid length （aa）	等电点 PI	分子量 Molecular weight （kDa）	不稳定指数 Instability index	疏水性指数 GRAVY	脂肪指数 Aliphatic index	跨膜结构数目 No. of transmembrane domains
MS.gene99860	MsCAX1	460	5.52	49.87385	44.42	0.516	104.72	11
MS.gene83511	MsCAX2	446	5.41	48.36603	44.32	0.544	105.81	11
MS.gene067498	MsCAX3	464	5.62	50.36244	44.47	0.511	104.44	11
MS.gene70485	MsCAX4	407	5.20	44.38009	37.15	0.562	120.69	9
MS.gene044358	MsCAX5	367	5.50	39.90768	34.51	0.483	120.84	8
MS.gene044315	MsCAX6	442	5.21	48.20153	34.66	0.570	117.08	9
MS.gene057847	MsCAX7	457	5.36	50.22957	29.72	0.524	116.56	10
MS.gene43800	MsCAX8	434	6.50	47.51891	31.02	0.609	121.98	10
MS.gene44897	MsCAX9	434	6.50	47.54693	30.85	0.608	121.98	10
MS.gene009878	MsCAX10	434	6.50	47.50088	31.46	0.615	122.88	10
MS.gene88788	MsCAX11	420	6.30	45.83903	28.84	0.656	126.98	10
MS.gene84200	MsCAX12	455	5.74	49.23152	37.33	0.580	123.25	11
MS.gene77339	MsCAX13	455	5.74	49.23355	38.06	0.582	122.62	11
MS.gene92638	MsCAX14	455	5.74	49.23355	38.06	0.582	122.62	11
MS.gene78431	MsCAX15	455	5.74	49.22955	36.91	0.586	123.47	11

蛋白质 Protein	α-螺旋 α-helix	β-转角 β-turn	无规则卷曲 Random coli	延伸链 Extended strand	蛋白质 Protein	α-螺旋 α-helix	β-转角 β-turn	无规则卷曲 Random coli	延伸链 Extended strand
MsCAX1	50.43	2.61	33.48	13.48	MsCAX9	52.30	2.53	29.95	15.21
MsCAX2	50.45	2.69	31.84	15.02	MsCAX10	55.30	3.23	27.42	14.06
MsCAX3	48.71	2.59	33.84	14.87	MsCAX11	52.29	3.57	27.39	14.76
MsCAX4	56.02	3.19	25.80	14.99	MsCAX12	48.57	2.86	30.33	18.27
MsCAX5	53.13	2.72	28.34	15.80	MsCAX13	52.53	2.20	30.99	14.29
MsCAX6	48.87	3.85	29.86	17.42	MsCAX14	51.87	2.20	31.43	14.51
MsCAX7	48.36	3.06	29.54	19.04	MsCAX15	49.45	3.08	31.21	16.26
MsCAX8	56.68	2.76	26.27	14.29