Genome-wide identification and expression analysis of expansin gene family in corm expansion of Colocasia esculenta

doi:10.3969/j.issn.1004-1524.20220960

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (7): 1604-1616.DOI: 10.3969/j.issn.1004-1524.20220960

• Horticultural Science • Previous Articles Next Articles

Genome-wide identification and expression analysis of expansin gene family in corm expansion of Colocasia esculenta

LI Bicong¹^,²(), LI Huiying¹^,², XIAO Yao¹^,², LUO Sha¹^,², ZHOU Qinghong¹^,², HUANG Yingjin¹^,², ZHU Qianglong¹^,²^,^*()

1. College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
2. Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Nanchang 330045, China

Received:2022-06-26 Online:2023-07-25 Published:2023-08-17
Contact: ZHU Qianglong

Abstract

Abstract:

Expansin is a group of proteins that can promote cell wall elongation and increase cell wall flexibility. The study identified the expansin gene family at taro whole genome, and analyzed the structural characteristics, phylogeny and expression pattern of the expansin gene family in taro corm expansion. The results showed that the whole taro genome contained 31 expansin genes, which were distributed at 8 chromosomes and 2 contigs. Phylogenetic tree analysis of all expansin genes in taro, Arabidopsis, rice and potato species showed that 31 expansin genes of taro were divided into four subfamilies, of which 23, 5, 1 and 2 expansin genes of taro were in EXPA, EXPB, EXLA and EXLB, respectively. Colinearity analysis showed that there were 7 pairs of colinear expansin genes between taro and Arabidopsis. Gene expression analysis showed that most members of the taro expansin gene family had low gene expression with no significant difference during taro corm expansion, but the five expansin genes (CeEXPA2, CeEXPA11, CeEXPA13, CeEXPA23 and CeEXLA1) had high gene expression with significant difference during taro corm expansion, suggesting that they could play important roles in regulating the corm expansion. The results of our study will help to understand the characteristics of the taro expansin gene family and its molecular function in taro corm expansion, and provide a theoretical basis for revealing the molecular regulation mechanism of taro corm growth and development.

Key words: Colocasia esculenta, expansin gene family, corm expansion

CLC Number:

S632.3

LI Bicong, LI Huiying, XIAO Yao, LUO Sha, ZHOU Qinghong, HUANG Yingjin, ZHU Qianglong. Genome-wide identification and expression analysis of expansin gene family in corm expansion of Colocasia esculenta[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1604-1616.

Figures/Tables 7

References 46

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基因名称Gene name	引物序列Primer sequence(5'→3')
CeEXPA2	F: CCTTGCTCTTCTTCTCCCTCTG; R: AAGCTCCACCCATTGTGCC
CeEXPA11	F: GCTGCTGCCATTTCTTTCTCA; R: ACCTCCATAGAAGGTGGCATG
CeEXPA13	F: GCTGAGTGAGGCTATGTTCGAG; R: GCTGAGTGAGGCTATGTTCGAG
CeEXPA23	F: GCTGCTGCCATTTCTTTCTCA; R: TCCACCCATTGTGCCAGAG
CeEXLA1	F: CCTCTTCCTGTCCTGCCTTCT; R: CCAAGGAGCCATACCCACAA
actin	F: CTAGTGGTCGCACAACAGGT; R: TTCACGCTCAGCAGTGGTAG

基因名称Gene name	引物序列Primer sequence(5'→3')
CeEXPA2	F: CCTTGCTCTTCTTCTCCCTCTG; R: AAGCTCCACCCATTGTGCC
CeEXPA11	F: GCTGCTGCCATTTCTTTCTCA; R: ACCTCCATAGAAGGTGGCATG
CeEXPA13	F: GCTGAGTGAGGCTATGTTCGAG; R: GCTGAGTGAGGCTATGTTCGAG
CeEXPA23	F: GCTGCTGCCATTTCTTTCTCA; R: TCCACCCATTGTGCCAGAG
CeEXLA1	F: CCTCTTCCTGTCCTGCCTTCT; R: CCAAGGAGCCATACCCACAA
actin	F: CTAGTGGTCGCACAACAGGT; R: TTCACGCTCAGCAGTGGTAG

基因名称 Gene names	基因序列号 Gene ID	染色体位置 Location	氨基酸长度 Length of protein/aa	信号肽 Signal peptide/ aa	分子量 Molecular weight/ku	理论等电点 pI	总平均疏水性 Grand average of hydropathicity (GRAVY)	蛋白不稳定 Instability index (Ⅱ)	脂溶指数 Aliphatic index (AI)	内含子数量 Number of intron	外显子数量 Number of exon	亚细胞定位 Subcellular localization
CeEXPA1	EVM0026182.1	chr01:200921296.. 200922918(+)	249	23	26.432 58	8.08	-0.055	35.9	67.15	2	3	细胞外 Extracellular
CeEXPA2	EVM0012344.1	chr01:202183325.. 202186948(-)	257	20	27.397 03	9.03	0.011	33.44	72.53	2	3	细胞外 Extracellular
CeEXPA3	EVM0024333.1	chr05:150932420.. 150934537(+)	269	22	29.240 10	9.70	-0.185	32.45	67.43	2	3	细胞外 Extracellular
CeEXPA4	EVM0006021.1	chr05:170577592.. 170579397(+)	270	-	29.416 22	6.43	-0.203	40.65	69.07	1	2	细胞外 Extracellular
CeEXPA5	EVM0027397.1	chr05:170583755.. 170584943(-)	243	27	25.661 22	8.54	0.151	38.89	76.3	1	2	细胞外 Extracellular
CeEXPA6	EVM0000590.1	chr05:170587143.. 170588191(-)	250	24	26.582 28	9.03	-0.002	32.79	71.48	1	2	细胞外 Extracellular
CeEXPA7	EVM0018716.1	chr05:170595320.. 170596335(+)	251	24	26.688 49	8.98	-0.031	31.42	71.16	1	2	细胞外 Extracellular
CeEXPA8	EVM0000741.1	chr05:170597431.. 170598613(+)	243	27	25.658 21	8.54	0.143	38.54	76.30	1	2	细胞外 Extracellular
CeEXPA9	EVM0004428.1	chr05:24336630.. 24338260(-)	242	23	25.840 91	8.08	-0.017	37.28	65.37	2	3	细胞外 Extracellular
CeEXPA10	EVM0003200.1	chr05:2472822.. 2474110(+)	247	20	25.953 08	7.58	0.039	31.64	71.13	2	3	细胞外 Extracellular
CeEXPA11	EVM0006482.1	chr06:89724779.. 89726644(+)	242	22	25.474 60	6.98	0.040	23.16	78.64	3	4	细胞外 Extracellular
CeEXPA12	EVM0017929.1	chr07:145329881.. 145331408(+)	310	-	34.004 85	9.13	-0.358	55.08	73.03	2	3	细胞外 Extracellular
CeEXPA13	EVM0001733.1	chr07:145471800.. 145473372(+)	307	-	33.605 43	8.83	-0.275	53.39	73.13	3	4	细胞外 Extracellular
CeEXPA14	EVM0014313.1	chr07:87019796.. 87023201(-)	287	-	31.198 69	8.98	0.008	37.82	78.82	2	3	细胞外 Extracellular
CeEXPA15	EVM0010866.1	chr07:88579339.. 88581309(-)	254	25	26.939 53	8.42	0.069	51.06	72.99	2	3	细胞外 Extracellular
CeEXPA16	EVM0014177.1	chr07:88694369.. 88696346(-)	254	25	26.939 53	8.42	0.069	51.06	72.99	2	3	细胞外 Extracellular
CeEXPA17	EVM0017235.1	chr08:25144199.. 25146621(-)	257	27	28.278 75	8.64	-0.291	29.81	61.48	3	4	细胞外 Extracellular
CeEXPA18	EVM0018313.1	chr09:153364305.. 153365614(-)	261	33	27.892 56	9.23	0.062	35.02	61.03	2	3	细胞外 Extracellular
CeEXPA19	EVM0012337.1	chr12:21154444.. 21155548(-)	285	28	31.574 69	9.01	-0.354	36.61	68.81	2	3	细胞外 Extracellular
CeEXPA20	EVM0025460.1	chr13:2511469.. 2512473(+)	251	26	26.690 07	8.78	-0.109	33.06	66.65	2	3	细胞外 Extracellular
CeEXPA21	EVM0024521.1	chr13:6625282.. 6626372(-)	247	26	26.799 49	9.24	-0.065	25.59	71.17	2	3	细胞外 Extracellular
CeEXPA22	EVM0003144.1	chr13:6823896.. 6825773(+)	259	26	27.757 24	7.48	-0.074	33.97	67.53	2	3	细胞外 Extracellular
CeEXPA23	EVM0023051.1	Contig09732:18818.. 21605(-)	257	22	27.425 84	9.25	-0.102	28.85	68.72	2	3	细胞外 Extracellular
CeEXPB1	EVM0002402.1	chr06:54257974.. 54259186(-)	290	-	29.923 40	6.02	0.018	45.28	66.03	3	4	细胞外 Extracellular
CeEXPB2	EVM0000778.1	chr06:54269693.. 54270918(-)	267	27	27.980 57	8.67	0.034	45.28	66.03	3	4	细胞外 Extracellular
CeEXPB3	EVM0011802.1	chr06:54278359.. 54279577(-)	260	25	26.663 96	8.39	0.079	36.77	69.50	3	4	细胞外 Extracellular
CeEXPB4	EVM0008727.1	chr06:54293245.. 54294599(-)	261	36	27.278 48	5.85	-0.071	54.75	68.89	3	4	细胞外 Extracellular
CeEXPB5	EVM0016278.1	chr07:142847771.. 142852026(-)	263	27	28.890 93	8.81	-0.190	48.57	70.46	3	4	细胞外 Extracellular
CeEXLA1	EVM0003292.1	chr13:17445338.. 17447787(+)	262	19	28.263 43	8.55	0.043	33.82	80.04	4	5	细胞外 Extracellular
CeEXLB1	EVM0028468.1	chr01:10814898.. 10817362(-)	247	18	16.753 37	5.95	-0.22	41.41	76.19	3	4	细胞外 Extracellular
CeEXLB2	EVM0005790.1	Contig01299:473365.. 475635(+)	259	25	27.487 76	4.84	-0.013	35.15	76.10	4	5	细胞外 Extracellular

基因名称 Gene names	基因序列号 Gene ID	染色体位置 Location	氨基酸长度 Length of protein/aa	信号肽 Signal peptide/ aa	分子量 Molecular weight/ku	理论等电点 pI	总平均疏水性 Grand average of hydropathicity (GRAVY)	蛋白不稳定 Instability index (Ⅱ)	脂溶指数 Aliphatic index (AI)	内含子数量 Number of intron	外显子数量 Number of exon	亚细胞定位 Subcellular localization
CeEXPA1	EVM0026182.1	chr01:200921296.. 200922918(+)	249	23	26.432 58	8.08	-0.055	35.9	67.15	2	3	细胞外 Extracellular
CeEXPA2	EVM0012344.1	chr01:202183325.. 202186948(-)	257	20	27.397 03	9.03	0.011	33.44	72.53	2	3	细胞外 Extracellular
CeEXPA3	EVM0024333.1	chr05:150932420.. 150934537(+)	269	22	29.240 10	9.70	-0.185	32.45	67.43	2	3	细胞外 Extracellular
CeEXPA4	EVM0006021.1	chr05:170577592.. 170579397(+)	270	-	29.416 22	6.43	-0.203	40.65	69.07	1	2	细胞外 Extracellular
CeEXPA5	EVM0027397.1	chr05:170583755.. 170584943(-)	243	27	25.661 22	8.54	0.151	38.89	76.3	1	2	细胞外 Extracellular
CeEXPA6	EVM0000590.1	chr05:170587143.. 170588191(-)	250	24	26.582 28	9.03	-0.002	32.79	71.48	1	2	细胞外 Extracellular
CeEXPA7	EVM0018716.1	chr05:170595320.. 170596335(+)	251	24	26.688 49	8.98	-0.031	31.42	71.16	1	2	细胞外 Extracellular
CeEXPA8	EVM0000741.1	chr05:170597431.. 170598613(+)	243	27	25.658 21	8.54	0.143	38.54	76.30	1	2	细胞外 Extracellular
CeEXPA9	EVM0004428.1	chr05:24336630.. 24338260(-)	242	23	25.840 91	8.08	-0.017	37.28	65.37	2	3	细胞外 Extracellular
CeEXPA10	EVM0003200.1	chr05:2472822.. 2474110(+)	247	20	25.953 08	7.58	0.039	31.64	71.13	2	3	细胞外 Extracellular
CeEXPA11	EVM0006482.1	chr06:89724779.. 89726644(+)	242	22	25.474 60	6.98	0.040	23.16	78.64	3	4	细胞外 Extracellular
CeEXPA12	EVM0017929.1	chr07:145329881.. 145331408(+)	310	-	34.004 85	9.13	-0.358	55.08	73.03	2	3	细胞外 Extracellular
CeEXPA13	EVM0001733.1	chr07:145471800.. 145473372(+)	307	-	33.605 43	8.83	-0.275	53.39	73.13	3	4	细胞外 Extracellular
CeEXPA14	EVM0014313.1	chr07:87019796.. 87023201(-)	287	-	31.198 69	8.98	0.008	37.82	78.82	2	3	细胞外 Extracellular
CeEXPA15	EVM0010866.1	chr07:88579339.. 88581309(-)	254	25	26.939 53	8.42	0.069	51.06	72.99	2	3	细胞外 Extracellular
CeEXPA16	EVM0014177.1	chr07:88694369.. 88696346(-)	254	25	26.939 53	8.42	0.069	51.06	72.99	2	3	细胞外 Extracellular
CeEXPA17	EVM0017235.1	chr08:25144199.. 25146621(-)	257	27	28.278 75	8.64	-0.291	29.81	61.48	3	4	细胞外 Extracellular
CeEXPA18	EVM0018313.1	chr09:153364305.. 153365614(-)	261	33	27.892 56	9.23	0.062	35.02	61.03	2	3	细胞外 Extracellular
CeEXPA19	EVM0012337.1	chr12:21154444.. 21155548(-)	285	28	31.574 69	9.01	-0.354	36.61	68.81	2	3	细胞外 Extracellular
CeEXPA20	EVM0025460.1	chr13:2511469.. 2512473(+)	251	26	26.690 07	8.78	-0.109	33.06	66.65	2	3	细胞外 Extracellular
CeEXPA21	EVM0024521.1	chr13:6625282.. 6626372(-)	247	26	26.799 49	9.24	-0.065	25.59	71.17	2	3	细胞外 Extracellular
CeEXPA22	EVM0003144.1	chr13:6823896.. 6825773(+)	259	26	27.757 24	7.48	-0.074	33.97	67.53	2	3	细胞外 Extracellular
CeEXPA23	EVM0023051.1	Contig09732:18818.. 21605(-)	257	22	27.425 84	9.25	-0.102	28.85	68.72	2	3	细胞外 Extracellular
CeEXPB1	EVM0002402.1	chr06:54257974.. 54259186(-)	290	-	29.923 40	6.02	0.018	45.28	66.03	3	4	细胞外 Extracellular
CeEXPB2	EVM0000778.1	chr06:54269693.. 54270918(-)	267	27	27.980 57	8.67	0.034	45.28	66.03	3	4	细胞外 Extracellular
CeEXPB3	EVM0011802.1	chr06:54278359.. 54279577(-)	260	25	26.663 96	8.39	0.079	36.77	69.50	3	4	细胞外 Extracellular
CeEXPB4	EVM0008727.1	chr06:54293245.. 54294599(-)	261	36	27.278 48	5.85	-0.071	54.75	68.89	3	4	细胞外 Extracellular
CeEXPB5	EVM0016278.1	chr07:142847771.. 142852026(-)	263	27	28.890 93	8.81	-0.190	48.57	70.46	3	4	细胞外 Extracellular
CeEXLA1	EVM0003292.1	chr13:17445338.. 17447787(+)	262	19	28.263 43	8.55	0.043	33.82	80.04	4	5	细胞外 Extracellular
CeEXLB1	EVM0028468.1	chr01:10814898.. 10817362(-)	247	18	16.753 37	5.95	-0.22	41.41	76.19	3	4	细胞外 Extracellular
CeEXLB2	EVM0005790.1	Contig01299:473365.. 475635(+)	259	25	27.487 76	4.84	-0.013	35.15	76.10	4	5	细胞外 Extracellular

Genome-wide identification and expression analysis of expansin gene family in corm expansion of Colocasia esculenta

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[1]	HONG Xia, ZHAO Yongbin, QU Weidong, CHEN Yinlong, QIU Liping, WANG Jiaoyang. Comparative analysis on genetic diversity of Colocasia esculenta germplasm in Zhejiang Province based on phenotype and simple sequence repeats markers [J]. , 2020, 32(9): 1544-1554.
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