Identification of LEA Family and Expression Analysis of Some Members Under Low-temperature Stress in Chinese Cabbage

doi:10.16420/j.issn.0513-353x.2021-0044

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (2): 304-318.doi: 10.16420/j.issn.0513-353x.2021-0044

• Research Papers • Previous Articles Next Articles

Identification of LEA Family and Expression Analysis of Some Members Under Low-temperature Stress in Chinese Cabbage

WANG Guangpeng, LIU Tongkun, XU Xinfeng, LI Zhubo, GAO Zhanyuan, HOU Xilin()

State Key Laboratory of Crop Genetics & Germplasm Enhancement,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops（East China）,Ministry of Agriculture and Rural Affairs,Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops,Ministry of Education,Nanjing 210095,China

Received:2021-04-06 Revised:2021-10-14 Online:2022-02-25 Published:2022-02-28
Contact: HOU Xilin E-mail:hxl@njau.edu.cn

Abstract

Abstract:

This study was based on the whole genome data of Chinese cabbage to identify and bioinformatics the late embryogenesis abundant protein（LEA）family genes. The sequence characteristics,gene structure,promoter cis-acting elements,chromosome localization,evolutionary relationships,and expression patterns in different tissues and under low temperature stress were investigated. The results showed that 65 family members were identified from the Chinese cabbage genome and could be divided into eight groups according to phylogenetic and conserved motif analysis. Fewer introns are prevalent and unevenly distributed on ten chromosomes,with three other members located on the Scaffold. The promoter cis-acting element analysis showed that 29 members（44.6%）had low temperature response elements. In addition,the proportion of light response elements and hormone response elements was the highest. The collinearity analysis showed that BrLEAs and AtLEAs had higher homology and were conservative in evolution. Analysis of transcriptome data of different tissues of Chinese cabbage found that the expression of BrLEA genes in different tissues was different and had tissue specificity. The expression of 13 family members under low temperature stress family members showed that the expression of low temperature stress increased.

Key words: Chinese cabbage, gene family of LEA, low temperature stress, bioinformatics

CLC Number:

S634.1

WANG Guangpeng, LIU Tongkun, XU Xinfeng, LI Zhubo, GAO Zhanyuan, HOU Xilin. Identification of LEA Family and Expression Analysis of Some Members Under Low-temperature Stress in Chinese Cabbage[J]. Acta Horticulturae Sinica, 2022, 49(2): 304-318.

Figures/Tables 8

References 42

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基因 ID Gene ID	基因名称 Gene name	引物序列（5′-3′） Primer sequence
Bra008242	BrDehydrin2	F：GGAATCATCAGCGGAGGTCA;R：CCTCGTGTTTAACCTCAGGCA
Bra025819	BrDehydrin4	F：TTCCGGTGAAGGAGGAAACG;R：CCGTGTCGACCACTTGAGAA
Bra012230	BrDehydrin5	F：TTCACCGATCCAACAGCTCC;R：CCTCCGTGTTGACGACTTGA
Bra015779	BrDehydrin6	F：AGGAATCATCAACGGCCACC;R：CACCGGCTCTGAGATGTGAA
Bra003732	BrDehydrin7	F：AGGACACGGAAAGAAACCCG;R：CCTCAACGGTCTTTGAGTGG
Bra013992	BrDehydrin8	F：TGCAGCTTCCAAAGGTTGTG;R：CGTCGCGTCAGTCACATAGA
Bra035491	BrLEA_1-3	F：GGGCACGGACTAAAGAGGAG;R：TCACAGGTGTGTGATGAGGC
Bra000414	BrLEA_2-2	F：AAGGACGATAGCGTCGGGTA;R：CCGCTATGCTATAGGCCACC
Bra026541	BrLEA_4-3	F：GAATGCGACCATTACACCGC;R：CCACTTCACTCCCCATGTCC
Bra000263	BrLEA_4-6	F：GGCCTTGAAAAATGGCGAGA;R：TTTGTGGCGTCCTTAGCCTC
Bra000265	BrLEA_4-7	F：CTCAGGAGCTGTTCTCAGTGG;R：ATCAACGACTTCTTGCGCTG
Bra000173	BrLEA_5-1	F：GCCGAGGAGGGAATACAAGG;R：TGGGTTCGTCCATCTCCTCT
Bra022950	BrLEA_6-1	F：GCCACTAGAAACGAGTCCGTA;R：GGCCATGCTTAACCTGTTGG
	Actin	F：AGGCTACACGTTCGGACAAG;R：TGGGGCACTAAACACAGTCA

基因 ID Gene ID	基因名称 Gene name	引物序列（5′-3′） Primer sequence
Bra008242	BrDehydrin2	F：GGAATCATCAGCGGAGGTCA;R：CCTCGTGTTTAACCTCAGGCA
Bra025819	BrDehydrin4	F：TTCCGGTGAAGGAGGAAACG;R：CCGTGTCGACCACTTGAGAA
Bra012230	BrDehydrin5	F：TTCACCGATCCAACAGCTCC;R：CCTCCGTGTTGACGACTTGA
Bra015779	BrDehydrin6	F：AGGAATCATCAACGGCCACC;R：CACCGGCTCTGAGATGTGAA
Bra003732	BrDehydrin7	F：AGGACACGGAAAGAAACCCG;R：CCTCAACGGTCTTTGAGTGG
Bra013992	BrDehydrin8	F：TGCAGCTTCCAAAGGTTGTG;R：CGTCGCGTCAGTCACATAGA
Bra035491	BrLEA_1-3	F：GGGCACGGACTAAAGAGGAG;R：TCACAGGTGTGTGATGAGGC
Bra000414	BrLEA_2-2	F：AAGGACGATAGCGTCGGGTA;R：CCGCTATGCTATAGGCCACC
Bra026541	BrLEA_4-3	F：GAATGCGACCATTACACCGC;R：CCACTTCACTCCCCATGTCC
Bra000263	BrLEA_4-6	F：GGCCTTGAAAAATGGCGAGA;R：TTTGTGGCGTCCTTAGCCTC
Bra000265	BrLEA_4-7	F：CTCAGGAGCTGTTCTCAGTGG;R：ATCAACGACTTCTTGCGCTG
Bra000173	BrLEA_5-1	F：GCCGAGGAGGGAATACAAGG;R：TGGGTTCGTCCATCTCCTCT
Bra022950	BrLEA_6-1	F：GCCACTAGAAACGAGTCCGTA;R：GGCCATGCTTAACCTGTTGG
	Actin	F：AGGCTACACGTTCGGACAAG;R：TGGGGCACTAAACACAGTCA

基因号 Gene number	基因名称 Gene name	氨基酸长度 Amino acid length	等电点 pI	分子量/D MW	不稳定性指数 Instability index	脂肪族指数 Aliphatic index	亲水性 GRAVY	亚细胞定位 Subcellular localization
Bra011874	BrDehydrin-1	149	5.65	15 928.40	23.71	58.93	-0.863	细胞核 Nucleus
Bra036843	BrDehydrin-10	134	9.19	13 834.22	42.98	49.55	-0.887	细胞核 Nucleus
Bra037177	BrDehydrin-11	144	8.81	15 139.46	45.61	33.26	-1.360	细胞核 Nucleus
Bra008242	BrDehydrin-2	194	5.52	21 840.38	62.43	53.71	-1.352	细胞核 Nucleus
Bra031809	BrDehydrin-3	192	7.14	18 844.17	33.09	32.14	-1.021	细胞核 Nucleus
Bra025819	BrDehydrin-4	271	5.00	31 018.16	61.44	47.49	-1.508	细胞核 Nucleus
Bra012230	BrDehydrin-5	220	5.11	24 837.39	62.24	55.41	-1.399	细胞核 Nucleus
Bra015779	BrDehydrin-6	195	5.45	22 044.52	63.15	50.41	-1.455	细胞核 Nucleus
Bra003732	BrDehydrin-7	194	5.47	21 755.35	56.38	53.25	-1.308	细胞核 Nucleus
Bra013992	BrDehydrin-8	257	6.17	28 978.00	34.53	35.33	-1.645	细胞核 Nucleus
Bra031192	BrDehydrin-9	183	6.49	19 183.88	36.64	49.18	-1.016	细胞核 Nucleus
Bra005911	BrLEA_1-1	159	9.22	16 286.99	17.53	43.71	-0.789	细胞核 Nucleus
Bra005353	BrLEA_1-2	98	9.22	10 666.89	42.18	49.18	-1.115	细胞核 Nucleus
Bra035491	BrLEA_1-3	132	9.68	14 933.95	56.61	51.89	-1.109	线粒体 Mitochondrion
Bra023278	BrLEA_1-4	133	9.24	14 507.53	59.47	48.65	-0.878	线粒体 Mitochondrion
Bra009225	BrLEA_1-5	159	8.93	16 180.83	16.45	38.81	-0.818	细胞核 Nucleus
Bra000339	BrLEA_2-1	777	9.02	84 314.53	32.33	96.22	-0.135	叶绿体 Chloroplast
Bra000414	BrLEA_2-2	166	4.81	17 823.38	17.04	96.81	0.030	胞外Extracellular
Bra039288	BrLEA_2-3	166	4.50	18 119.88	16.96	100.36	0.013	叶绿体 Chloroplast
Bra037669	BrLEA_2-4	506	8.85	55 465.06	27.06	85.89	-0.399	细胞核 Nucleus
Bra004565	BrLEA_2-5	166	4.81	17 725.34	20.39	106.20	0.093	细胞膜 Cell membrane
Bra030494	BrLEA_2-6	151	4.72	16 404.92	10.57	106.42	0.075	细胞膜 Cell membrane
Bra033520	BrLEA_3-1	99	9.72	10 582.01	50.01	70.10	-0.400	叶绿体 Chloroplast
Bra000884	BrLEA_3-2	94	9.85	10 095.53	39.42	78.94	-0.349	叶绿体 Chloroplast
Bra014864	BrLEA_3-3	122	9.20	14 152.16	50.98	63.20	-0.598	叶绿体 Chloroplast
Bra018556	BrLEA_3-4	93	9.99	10 112.56	52.38	72.47	-0.482	叶绿体 Chloroplast
Bra038061	BrLEA_3-5	57	4.94	6 614.40	49.22	56.67	-0.912	线粒体 Mitochondrion
Bra036272	BrLEA_3-6	94	9.99	10 088.55	43.90	72.77	-0.299	叶绿体 Chloroplast
Bra033350	BrLEA_3-7	98	8.03	10 298.59	40.91	76.84	-0.229	叶绿体 Chloroplast
Bra021126	BrLEA_4-1	226	9.02	24 598.55	28.79	22.79	-1.475	线粒体 Mitochondrion
Bra022221	BrLEA_4-10	298	5.45	32 431.59	30.10	54.50	-1.126	胞外Extracellular
Bra027219	BrLEA_4-11	229	8.83	24 810.86	27.04	22.97	-1.414	线粒体 Mitochondrion
Bra005256	BrLEA_4-12	399	5.74	43 565.34	20.90	52.93	-0.970	细胞膜 Cell membrane
Bra019628	BrLEA_4-13	451	5.20	48 554.47	12.26	47.98	-1.141	细胞核 Nucleus
Bra025130	BrLEA_4-14	201	5.40	22 054.03	38.33	77.21	-0.429	叶绿体 Chloroplast
Bra039616	BrLEA_4-15	480	6.47	52 652.67	18.82	47.04	-0.921	叶绿体 Chloroplast
Bra010561	BrLEA_4-16	487	5.63	52 431.94	23.72	46.65	-0.923	叶绿体 Chloroplast
Bra020879	BrLEA_4-17	218	5.12	24 376.73	15.32	38.72	-1.441	细胞核 Nucleus
Bra027542	BrLEA_4-18	311	7.60	35 005.70	23.66	43.79	-1.371	叶绿体 Chloroplast
Bra037225	BrLEA_4-19	722	8.58	80 928.05	43.18	68.66	-0.722	叶绿体 Chloroplast
Bra013489	BrLEA_4-2	253	8.55	27 837.93	20.67	47.31	-1.202	叶绿体 Chloroplast
Bra036021	BrLEA_4-20	253	5.72	28 430.30	32.23	43.72	-1.355	叶绿体 Chloroplast
Bra041061	BrLEA_4-21	241	6.17	26 330.13	20.46	50.83	-1.111	叶绿体 Chloroplast
Bra026541	BrLEA_4-3	192	8.57	20 399.00	33.96	62.55	-0.669	叶绿体 Chloroplast
Bra008006	BrLEA_4-4	462	9.03	50 701.68	32.68	78.53	-0.390	胞外Extracellular
Bra001666	BrLEA_4-5	276	5.54	30 311.37	25.62	53.22	-1.093	叶绿体 Chloroplast
Bra000263	BrLEA_4-6	142	8.65	14 760.62	19.57	77.75	-0.430	叶绿体 Chloroplast
Bra000265	BrLEA_4-7	129	5.31	13 894.51	22.81	71.86	-0.692	叶绿体 Chloroplast
Bra017229	BrLEA_4-8	398	6.02	43 386.25	20.77	55.63	-1.065	细胞核 Nucleus
Bra016868	BrLEA_4-9	679	5.98	72 972.61	33.88	45.77	-1.088	细胞核 Nucleus
Bra000173	BrLEA_5-1	88	5.88	9 630.38	37.14	25.57	-1.659	线粒体 Mitochondrion
Bra004981	BrLEA_5-2	84	6.74	9 264.98	49.89	27.96	-1.704	线粒体 Mitochondrion
Bra040894	BrLEA_5-3	172	6.17	18 997.70	42.85	30.64	-1.635	细胞核 Nucleus
Bra022950	BrLEA_6-1	71	6.03	7 581.23	52.98	40.00	-1.238	细胞核 Nucleus
Bra021869	BrLEA_6-2	72	5.21	7 627.30	58.73	40.83	-1.174	细胞核 Nucleus
Bra039946	BrLEA_6-3	82	4.72	8 433.11	44.84	37.07	-1.055	线粒体 Mitochondrion
Bra022642	BrSMP-1	173	5.88	18 379.46	40.43	86.36	-0.357	细胞膜 Cell membrane
Bra020604	BrSMP-2	181	4.76	18 366.26	31.03	71.44	-0.481	细胞核 Nucleus
Bra001869	BrSMP-3	239	5.70	25 385.45	46.14	76.78	-0.380	细胞膜 Cell membrane
Bra029085	BrSMP-4	177	5.43	18 691.81	41.22	82.20	-0.351	细胞膜 Cell membrane
Bra039956	BrSMP-5	262	4.71	26 692.50	34.19	77.21	-0.239	细胞膜 Cell membrane
Bra009983	BrSMP-6	192	4.76	19 473.41	23.22	69.32	-0.515	细胞膜 Cell membrane
Bra036112	BrSMP-7	191	4.99	19 600.77	26.99	75.81	-0.414	细胞核 Nucleus
Bra033375	BrSMP-8	177	4.53	18 185.98	30.21	71.24	-0.540	叶绿体 Chloroplast
Bra033377	BrSMP-9	283	8.89	32 586.25	52.20	75.72	-0.543	叶绿体 Chloroplast

基因号 Gene number	基因名称 Gene name	氨基酸长度 Amino acid length	等电点 pI	分子量/D MW	不稳定性指数 Instability index	脂肪族指数 Aliphatic index	亲水性 GRAVY	亚细胞定位 Subcellular localization
Bra011874	BrDehydrin-1	149	5.65	15 928.40	23.71	58.93	-0.863	细胞核 Nucleus
Bra036843	BrDehydrin-10	134	9.19	13 834.22	42.98	49.55	-0.887	细胞核 Nucleus
Bra037177	BrDehydrin-11	144	8.81	15 139.46	45.61	33.26	-1.360	细胞核 Nucleus
Bra008242	BrDehydrin-2	194	5.52	21 840.38	62.43	53.71	-1.352	细胞核 Nucleus
Bra031809	BrDehydrin-3	192	7.14	18 844.17	33.09	32.14	-1.021	细胞核 Nucleus
Bra025819	BrDehydrin-4	271	5.00	31 018.16	61.44	47.49	-1.508	细胞核 Nucleus
Bra012230	BrDehydrin-5	220	5.11	24 837.39	62.24	55.41	-1.399	细胞核 Nucleus
Bra015779	BrDehydrin-6	195	5.45	22 044.52	63.15	50.41	-1.455	细胞核 Nucleus
Bra003732	BrDehydrin-7	194	5.47	21 755.35	56.38	53.25	-1.308	细胞核 Nucleus
Bra013992	BrDehydrin-8	257	6.17	28 978.00	34.53	35.33	-1.645	细胞核 Nucleus
Bra031192	BrDehydrin-9	183	6.49	19 183.88	36.64	49.18	-1.016	细胞核 Nucleus
Bra005911	BrLEA_1-1	159	9.22	16 286.99	17.53	43.71	-0.789	细胞核 Nucleus
Bra005353	BrLEA_1-2	98	9.22	10 666.89	42.18	49.18	-1.115	细胞核 Nucleus
Bra035491	BrLEA_1-3	132	9.68	14 933.95	56.61	51.89	-1.109	线粒体 Mitochondrion
Bra023278	BrLEA_1-4	133	9.24	14 507.53	59.47	48.65	-0.878	线粒体 Mitochondrion
Bra009225	BrLEA_1-5	159	8.93	16 180.83	16.45	38.81	-0.818	细胞核 Nucleus
Bra000339	BrLEA_2-1	777	9.02	84 314.53	32.33	96.22	-0.135	叶绿体 Chloroplast
Bra000414	BrLEA_2-2	166	4.81	17 823.38	17.04	96.81	0.030	胞外Extracellular
Bra039288	BrLEA_2-3	166	4.50	18 119.88	16.96	100.36	0.013	叶绿体 Chloroplast
Bra037669	BrLEA_2-4	506	8.85	55 465.06	27.06	85.89	-0.399	细胞核 Nucleus
Bra004565	BrLEA_2-5	166	4.81	17 725.34	20.39	106.20	0.093	细胞膜 Cell membrane
Bra030494	BrLEA_2-6	151	4.72	16 404.92	10.57	106.42	0.075	细胞膜 Cell membrane
Bra033520	BrLEA_3-1	99	9.72	10 582.01	50.01	70.10	-0.400	叶绿体 Chloroplast
Bra000884	BrLEA_3-2	94	9.85	10 095.53	39.42	78.94	-0.349	叶绿体 Chloroplast
Bra014864	BrLEA_3-3	122	9.20	14 152.16	50.98	63.20	-0.598	叶绿体 Chloroplast
Bra018556	BrLEA_3-4	93	9.99	10 112.56	52.38	72.47	-0.482	叶绿体 Chloroplast
Bra038061	BrLEA_3-5	57	4.94	6 614.40	49.22	56.67	-0.912	线粒体 Mitochondrion
Bra036272	BrLEA_3-6	94	9.99	10 088.55	43.90	72.77	-0.299	叶绿体 Chloroplast
Bra033350	BrLEA_3-7	98	8.03	10 298.59	40.91	76.84	-0.229	叶绿体 Chloroplast
Bra021126	BrLEA_4-1	226	9.02	24 598.55	28.79	22.79	-1.475	线粒体 Mitochondrion
Bra022221	BrLEA_4-10	298	5.45	32 431.59	30.10	54.50	-1.126	胞外Extracellular
Bra027219	BrLEA_4-11	229	8.83	24 810.86	27.04	22.97	-1.414	线粒体 Mitochondrion
Bra005256	BrLEA_4-12	399	5.74	43 565.34	20.90	52.93	-0.970	细胞膜 Cell membrane
Bra019628	BrLEA_4-13	451	5.20	48 554.47	12.26	47.98	-1.141	细胞核 Nucleus
Bra025130	BrLEA_4-14	201	5.40	22 054.03	38.33	77.21	-0.429	叶绿体 Chloroplast
Bra039616	BrLEA_4-15	480	6.47	52 652.67	18.82	47.04	-0.921	叶绿体 Chloroplast
Bra010561	BrLEA_4-16	487	5.63	52 431.94	23.72	46.65	-0.923	叶绿体 Chloroplast
Bra020879	BrLEA_4-17	218	5.12	24 376.73	15.32	38.72	-1.441	细胞核 Nucleus
Bra027542	BrLEA_4-18	311	7.60	35 005.70	23.66	43.79	-1.371	叶绿体 Chloroplast
Bra037225	BrLEA_4-19	722	8.58	80 928.05	43.18	68.66	-0.722	叶绿体 Chloroplast
Bra013489	BrLEA_4-2	253	8.55	27 837.93	20.67	47.31	-1.202	叶绿体 Chloroplast
Bra036021	BrLEA_4-20	253	5.72	28 430.30	32.23	43.72	-1.355	叶绿体 Chloroplast
Bra041061	BrLEA_4-21	241	6.17	26 330.13	20.46	50.83	-1.111	叶绿体 Chloroplast
Bra026541	BrLEA_4-3	192	8.57	20 399.00	33.96	62.55	-0.669	叶绿体 Chloroplast
Bra008006	BrLEA_4-4	462	9.03	50 701.68	32.68	78.53	-0.390	胞外Extracellular
Bra001666	BrLEA_4-5	276	5.54	30 311.37	25.62	53.22	-1.093	叶绿体 Chloroplast
Bra000263	BrLEA_4-6	142	8.65	14 760.62	19.57	77.75	-0.430	叶绿体 Chloroplast
Bra000265	BrLEA_4-7	129	5.31	13 894.51	22.81	71.86	-0.692	叶绿体 Chloroplast
Bra017229	BrLEA_4-8	398	6.02	43 386.25	20.77	55.63	-1.065	细胞核 Nucleus
Bra016868	BrLEA_4-9	679	5.98	72 972.61	33.88	45.77	-1.088	细胞核 Nucleus
Bra000173	BrLEA_5-1	88	5.88	9 630.38	37.14	25.57	-1.659	线粒体 Mitochondrion
Bra004981	BrLEA_5-2	84	6.74	9 264.98	49.89	27.96	-1.704	线粒体 Mitochondrion
Bra040894	BrLEA_5-3	172	6.17	18 997.70	42.85	30.64	-1.635	细胞核 Nucleus
Bra022950	BrLEA_6-1	71	6.03	7 581.23	52.98	40.00	-1.238	细胞核 Nucleus
Bra021869	BrLEA_6-2	72	5.21	7 627.30	58.73	40.83	-1.174	细胞核 Nucleus
Bra039946	BrLEA_6-3	82	4.72	8 433.11	44.84	37.07	-1.055	线粒体 Mitochondrion
Bra022642	BrSMP-1	173	5.88	18 379.46	40.43	86.36	-0.357	细胞膜 Cell membrane
Bra020604	BrSMP-2	181	4.76	18 366.26	31.03	71.44	-0.481	细胞核 Nucleus
Bra001869	BrSMP-3	239	5.70	25 385.45	46.14	76.78	-0.380	细胞膜 Cell membrane
Bra029085	BrSMP-4	177	5.43	18 691.81	41.22	82.20	-0.351	细胞膜 Cell membrane
Bra039956	BrSMP-5	262	4.71	26 692.50	34.19	77.21	-0.239	细胞膜 Cell membrane
Bra009983	BrSMP-6	192	4.76	19 473.41	23.22	69.32	-0.515	细胞膜 Cell membrane
Bra036112	BrSMP-7	191	4.99	19 600.77	26.99	75.81	-0.414	细胞核 Nucleus
Bra033375	BrSMP-8	177	4.53	18 185.98	30.21	71.24	-0.540	叶绿体 Chloroplast
Bra033377	BrSMP-9	283	8.89	32 586.25	52.20	75.72	-0.543	叶绿体 Chloroplast

Identification of LEA Family and Expression Analysis of Some Members Under Low-temperature Stress in Chinese Cabbage

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