芋扩展蛋白基因家族的全基因组鉴定及其在球茎膨大中的表达分析

doi:10.3969/j.issn.1004-1524.20220960

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (7): 1604-1616.DOI: 10.3969/j.issn.1004-1524.20220960

芋扩展蛋白基因家族的全基因组鉴定及其在球茎膨大中的表达分析

李必聪¹^,²(), 李慧英¹^,², 肖遥¹^,², 罗莎¹^,², 周庆红¹^,², 黄英金¹^,², 朱强龙¹^,²^,^*()

1.江西农业大学农学院,江西南昌 330045
2.江西省薯芋生物学重点实验室,江西南昌 330045

收稿日期:2022-06-26 出版日期:2023-07-25 发布日期:2023-08-17
作者简介:李必聪(1997—),男,江西抚州人,博士研究生,研究方向为薯芋生物学研究。E-mail: lbc012138@163.com
通讯作者: *朱强龙,E-mail: longzhu2011@126.com
基金资助:
国家自然科学基金(32060683);江西省自然科学基金(20202ACBL215006);江西重点研发计划(20212BBF61001);江西省人力资源和计会保障厅博士后科研择优资助项目(2021KY38)

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

摘要/Abstract

摘要：

扩展蛋白是一类具有促进细胞壁伸长和增加细胞壁柔韧性作用的蛋白。本研究基于芋全基因组范围鉴定扩展蛋白基因,并分析该家族基因结构特征、系统发育及其在芋球茎膨大中的表达模式。结果表明,芋全基因组包含31个扩展蛋白基因,分布在芋8条染色体及2个重叠群上。在芋和拟南芥、水稻、马铃薯等4个物种中的扩展蛋白基因进行系统发育树分析中,所有的扩展蛋白基因划分到4个亚家族中,其中EXPA有23个,EXPB有5个,EXLA有1个,EXLB有2个。共线性分析表明,芋和拟南芥之间存在7对共线性扩展蛋白基因。基因表达分析发现,芋扩展蛋白基因家族不同成员在不同组织中有不同的表达模式,其中CeEXPA2、CeEXPA11、CeEXPA13、CeEXPA23和CeEXLA1等5个基因在球茎膨大过程中高表达且差异显著,表明它们可能对芋球茎的膨大发挥了重要的调控作用。本研究结果将有助于了解芋扩展蛋白基因家族的特征及其在球茎膨大中的分子功能,为揭示芋球茎生长发育的分子调控机理提供理论依据。

关键词: 芋, 扩展蛋白基因家族, 球茎膨大

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

中图分类号:

S632.3

李必聪, 李慧英, 肖遥, 罗莎, 周庆红, 黄英金, 朱强龙. 芋扩展蛋白基因家族的全基因组鉴定及其在球茎膨大中的表达分析[J]. 浙江农业学报, 2023, 35(7): 1604-1616.

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.

图/表 7

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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

芋扩展蛋白基因家族的全基因组鉴定及其在球茎膨大中的表达分析

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

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