甜瓜SWEET基因家族的全基因组鉴定及生物信息学分析

doi:10.3969/j.issn.1004-1524.20220943

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (7): 1591-1603.DOI: 10.3969/j.issn.1004-1524.20220943

甜瓜SWEET基因家族的全基因组鉴定及生物信息学分析

寿伟松(), 何艳军, 沈佳, 许昕阳

浙江省农业科学院蔬菜研究所,浙江杭州 310021

收稿日期:2022-06-23 出版日期:2023-07-25 发布日期:2023-08-17
作者简介:寿伟松(1972—),男,浙江绍兴人,硕士,副研究员,主要从事西甜瓜育种与栽培。E-mail: shouws@zaas.ac.cn
基金资助:
浙江省第三次全国农作物种质资源普查与收集行动(111821301354052030);浙江省农业(蔬菜新品种选育)新品种选育重大科技专项(2021C02065-3-2);国家自然科学基金(31872130)

Genome-wide identification and bioinformatics analysis of SWEET gene family in melon

SHOU Weisong(), HE Yanjun, SHEN Jia, XU Xinyang

Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2022-06-23 Online:2023-07-25 Published:2023-08-17

摘要/Abstract

摘要：

糖外排转运子(sugars will eventually be exported transporter,SWEET)是一类新型的糖转运蛋白,其在植物生长发育、植物与病原体互作以及植物胁迫耐受性方面都起着重要作用。基于甜瓜中还未有该家族基因的相关报道,本研究开展CmSWEET的全基因组鉴定和生物信息学分析。通过同源性搜索,总共鉴定到17个甜瓜CmSWEET基因。这些基因分布于甜瓜8条染色体上,具有典型的MtN3/saliva结构域。系统发育树将拟南芥、黄瓜和甜瓜的SWEET蛋白分为4个进化分支,其中亚族Ⅲ是甜瓜和黄瓜独有的亚族。基因启动子区域的顺式作用元件显示,CmSWEET含有许多与植物激素和应激相关的调节元件,暗示了CmSWEET在参与调节甜瓜生长发育以及环境适应性方面有重要作用。基因表达量分析表明,大部分CmSWEET基因在花(雌花和雄花)和根中高表达,部分CmSWEET基因在果实发育时期表达量较高。此外,RNA-Seq结果暗示,CmSWEET基因可能参与对尖孢镰刀菌和白粉病菌侵染的抗性响应。本研究为今后探究CmSWEET蛋白在甜瓜生长发育过程以及响应生物和非生物胁迫中的分子功能奠定了坚实的基础。

关键词: 甜瓜, 糖外排转运子, 全基因组鉴定, 进化分析

Abstract:

Sugars will eventually be exported transporter (SWEET) is a novel family of sugar transporters that are involved in plant growth and development, plant-pathogen interaction, and stress tolerance. Due to the lack of reports of SWEET family genes in melon, this study carried out the genome-wide identification and bioinformatics analysis of CmSWEET. A total of 17 melon CmSWEET genes were identified by homology search. These genes that distributed on 8 chromosomes all have a typical MtN3/saliva domain. Phylogenetic analysis classified the SWEET proteins of Arabidopsis, cucumber and melon into four evolutionary clades, of which subfamily Ⅲ is unique to melon and cucumber. The cis-acting elements in the gene promoter region showed that CmSWEET contains many regulatory elements related to plant hormones and stress, suggesting that CmSWEET plays an important role in regulating growth and environmental adaptation in melon. Tissue-specific analysis showed that most of the CmSWEET genes were highly expressed in female and male flowers and roots, and some CmSWEET genes were highly expressed during fruit development. Furthermore, RNA-Seq results suggested that CmSWEET genes might be involved in resistance to Fusarium oxysporum and powdery mildew infection. This study lays a solid foundation for future research into their molecular function of CmSWEET in melon developmental processes and responses to biotic and abiotic stresses.

Key words: melon, sugars will eventually be exported transporter, genome-wide identification, phylogenetic analysis

中图分类号:

S652

寿伟松, 何艳军, 沈佳, 许昕阳. 甜瓜SWEET基因家族的全基因组鉴定及生物信息学分析[J]. 浙江农业学报, 2023, 35(7): 1591-1603.

SHOU Weisong, HE Yanjun, SHEN Jia, XU Xinyang. Genome-wide identification and bioinformatics analysis of SWEET gene family in melon[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1591-1603.

图/表 11

参考文献 34

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基因名称 Gene name	基因ID Gene ID	染色体位置 Chromosome location	氨基酸长度 Protein length/aa	跨膜结构域 Transmembrane domains	亚细胞定位 Subcellular localization	蛋白分子量 Molecular weight/ku	等电点 Isoelectric point
CmSWEET01	MELO3C027076.2	chr00 : 2 331 064.. 2 333 983 (+)	204	4	细胞膜 Plasma membrane	22.53	8.38
CmSWEET02	MELO3C000200.2	chr00 : 10 680 046.. 10 682 566 (+)	193	4	液泡膜 Vocuole membrane	21.61	8.02
CmSWEET03	MELO3C026184.2	chr02 : 26 865 472.. 26 867 397 (-)	296	7	细胞膜 Plasma membrane	33.01	9.59
CmSWEET04	MELO3C026183.2	chr02 : 26 872 431.. 26 874 105 (-)	297	7	细胞膜 Plasma membrane	33.35	8.69
CmSWEET05	MELO3C008417.2	chr03 : 5 749 431.. 5 757 783 (+)	252	7	细胞膜 Plasma membrane	27.66	4.50
CmSWEET06	MELO3C009951.2	chr04 : 27 842 743.. 27 847 975 (-)	248	7	细胞膜 Plasma membrane	28.20	8.90
CmSWEET07	MELO3C009950.2	chr04 : 27 855 027.. 27 857 570 (-)	234	7	细胞膜 Plasma membrane	26.02	8.66
CmSWEET08	MELO3C008674.2	chr05 : 16 922 222.. 16 926 703 (-)	262	7	细胞膜 Plasma membrane	30.09	9.34
CmSWEET09	MELO3C031232.2	chr05 : 16 940 142.. 16 943 300 (-)	212	6	细胞膜 Plasma membrane	24.30	10.20
CmSWEET10	MELO3C004222.2	chr05 : 25 333 995.. 25 335 673 (-)	151	5	液泡膜 Vacuole membrane	16.59	8.84
CmSWEET11	MELO3C016259.2	chr07 : 22 840 158.. 22843162 (+)	262	7	细胞膜 Plasma membrane	29.08	9.28
CmSWEET12	MELO3C005758.2	chr09 : 24023344.. 24025966 (+)	265	7	细胞膜 Plasma membrane	29.15	10.04
CmSWEET13	MELO3C005869.2	chr09 : 24871177.. 24874018 (+)	208	5	细胞膜 Plasma membrane	23.51	9.15
CmSWEET14	MELO3C022341.2	chr11 : 32980155.. 32982488 (-)	273	6	细胞膜 Plasma membrane	30.88	9.37
CmSWEET15	MELO3C002381.2	chr12 : 24451493.. 24453403 (+)	291	7	内质网 Endoplasmic reticulum	32.87	6.95
CmSWEET16	MELO3C002380.2	chr12 : 24461695.. 24463640 (+)	242	5	细胞膜 Plasma membrane	27.38	9.22
CmSWEET17	MELO3C002256.2	chr12 : 25307536.. 25308775 (-)	183	5	细胞膜 Plasma membrane	21.03	9.67

基因名称 Gene name	基因ID Gene ID	染色体位置 Chromosome location	氨基酸长度 Protein length/aa	跨膜结构域 Transmembrane domains	亚细胞定位 Subcellular localization	蛋白分子量 Molecular weight/ku	等电点 Isoelectric point
CmSWEET01	MELO3C027076.2	chr00 : 2 331 064.. 2 333 983 (+)	204	4	细胞膜 Plasma membrane	22.53	8.38
CmSWEET02	MELO3C000200.2	chr00 : 10 680 046.. 10 682 566 (+)	193	4	液泡膜 Vocuole membrane	21.61	8.02
CmSWEET03	MELO3C026184.2	chr02 : 26 865 472.. 26 867 397 (-)	296	7	细胞膜 Plasma membrane	33.01	9.59
CmSWEET04	MELO3C026183.2	chr02 : 26 872 431.. 26 874 105 (-)	297	7	细胞膜 Plasma membrane	33.35	8.69
CmSWEET05	MELO3C008417.2	chr03 : 5 749 431.. 5 757 783 (+)	252	7	细胞膜 Plasma membrane	27.66	4.50
CmSWEET06	MELO3C009951.2	chr04 : 27 842 743.. 27 847 975 (-)	248	7	细胞膜 Plasma membrane	28.20	8.90
CmSWEET07	MELO3C009950.2	chr04 : 27 855 027.. 27 857 570 (-)	234	7	细胞膜 Plasma membrane	26.02	8.66
CmSWEET08	MELO3C008674.2	chr05 : 16 922 222.. 16 926 703 (-)	262	7	细胞膜 Plasma membrane	30.09	9.34
CmSWEET09	MELO3C031232.2	chr05 : 16 940 142.. 16 943 300 (-)	212	6	细胞膜 Plasma membrane	24.30	10.20
CmSWEET10	MELO3C004222.2	chr05 : 25 333 995.. 25 335 673 (-)	151	5	液泡膜 Vacuole membrane	16.59	8.84
CmSWEET11	MELO3C016259.2	chr07 : 22 840 158.. 22843162 (+)	262	7	细胞膜 Plasma membrane	29.08	9.28
CmSWEET12	MELO3C005758.2	chr09 : 24023344.. 24025966 (+)	265	7	细胞膜 Plasma membrane	29.15	10.04
CmSWEET13	MELO3C005869.2	chr09 : 24871177.. 24874018 (+)	208	5	细胞膜 Plasma membrane	23.51	9.15
CmSWEET14	MELO3C022341.2	chr11 : 32980155.. 32982488 (-)	273	6	细胞膜 Plasma membrane	30.88	9.37
CmSWEET15	MELO3C002381.2	chr12 : 24451493.. 24453403 (+)	291	7	内质网 Endoplasmic reticulum	32.87	6.95
CmSWEET16	MELO3C002380.2	chr12 : 24461695.. 24463640 (+)	242	5	细胞膜 Plasma membrane	27.38	9.22
CmSWEET17	MELO3C002256.2	chr12 : 25307536.. 25308775 (-)	183	5	细胞膜 Plasma membrane	21.03	9.67

基因名称 Gene name	激素响应相关元件数量 Number of hormone response-related element							应激响应相关元件数量 Number of stress response-related element
基因名称 Gene name	ABRE	TGA- element	CGTCA- motif	TGACG- motif	GARE- motif	P-box	TCA- element	ARE	GC- motif	MBS	TC-rich repeats	WUN- motif	MYB	MYC	W-box
CmSWEET01	0	0	1	1	0	0	1	0	0	0	1	0	2	1	0
CmSWEET02	3	0	1	1	1	0	0	1	0	0	1	0	3	2	0
CmSWEET03	3	0	1	1	1	0	1	3	0	1	0	0	4	2	1
CmSWEET04	1	0	0	0	0	1	1	2	0	0	0	0	4	3	0
CmSWEET05	3	0	0	0	0	0	0	1	0	0	0	0	6	1	0
CmSWEET06	0	1	2	2	0	0	0	1	0	1	1	0	2	4	1
CmSWEET07	1	2	1	1	0	0	0	0	0	0	0	0	1	2	0
CmSWEET08	7	2	0	0	0	0	0	3	1	0	0	0	1	3	0
CmSWEET09	1	2	1	1	0	0	4	5	0	0	1	1	3	4	3
CmSWEET10	0	0	1	1	0	0	0	3	0	0	2	5	1	4	0
CmSWEET11	1	0	2	2	0	0	0	0	0	0	2	0	2	7	0
CmSWEET12	1	0	2	2	0	0	1	2	0	0	0	0	2	2	0
CmSWEET13	2	0	0	0	0	2	0	1	0	0	0	0	4	4	1
CmSWEET14	1	0	0	0	0	1	1	1	0	1	1	0	2	4	0
CmSWEET15	3	0	0	1	0	1	0	2	0	0	0	1	1	2	1
CmSWEET16	1	1	0	0	0	1	1	2	0	0	1	0	2	2	0
CmSWEET17	0	0	0	0	0	0	1	3	0	1	1	0	4	3	0

基因名称 Gene name	激素响应相关元件数量 Number of hormone response-related element							应激响应相关元件数量 Number of stress response-related element
基因名称 Gene name	ABRE	TGA- element	CGTCA- motif	TGACG- motif	GARE- motif	P-box	TCA- element	ARE	GC- motif	MBS	TC-rich repeats	WUN- motif	MYB	MYC	W-box
CmSWEET01	0	0	1	1	0	0	1	0	0	0	1	0	2	1	0
CmSWEET02	3	0	1	1	1	0	0	1	0	0	1	0	3	2	0
CmSWEET03	3	0	1	1	1	0	1	3	0	1	0	0	4	2	1
CmSWEET04	1	0	0	0	0	1	1	2	0	0	0	0	4	3	0
CmSWEET05	3	0	0	0	0	0	0	1	0	0	0	0	6	1	0
CmSWEET06	0	1	2	2	0	0	0	1	0	1	1	0	2	4	1
CmSWEET07	1	2	1	1	0	0	0	0	0	0	0	0	1	2	0
CmSWEET08	7	2	0	0	0	0	0	3	1	0	0	0	1	3	0
CmSWEET09	1	2	1	1	0	0	4	5	0	0	1	1	3	4	3
CmSWEET10	0	0	1	1	0	0	0	3	0	0	2	5	1	4	0
CmSWEET11	1	0	2	2	0	0	0	0	0	0	2	0	2	7	0
CmSWEET12	1	0	2	2	0	0	1	2	0	0	0	0	2	2	0
CmSWEET13	2	0	0	0	0	2	0	1	0	0	0	0	4	4	1
CmSWEET14	1	0	0	0	0	1	1	1	0	1	1	0	2	4	0
CmSWEET15	3	0	0	1	0	1	0	2	0	0	0	1	1	2	1
CmSWEET16	1	1	0	0	0	1	1	2	0	0	1	0	2	2	0
CmSWEET17	0	0	0	0	0	0	1	3	0	1	1	0	4	3	0

基因名称 Gene name	光响应相关元件数量Number of light response-related element
基因名称 Gene name	GATA- motif	ATC- motif	Gap- box	ACE	Box 4	MRE	3-AF1 binding site	GA- motif	TCCC- motif	ATCT- motif	I- box	L- box	TCT- motif	G- box	chs- CMA1a	AT1- motif	AE- box	GT1- motif	AAAC- motif
CmSWEET01	2	0	0	0	8	0	0	0	0	1	0	0	0	1	1	1	0	0	1
CmSWEET02	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0
CmSWEET03	0	0	0	0	0	0	0	0	0	0	0	0	1	3	1	0	0	2	0
CmSWEET04	1	0	0	0	4	0	0	0	0	0	1	0	0	2	0	0	0	1	1
CmSWEET05	0	0	0	0	2	0	0	0	1	0	0	0	1	3	1	1	0	1	0
CmSWEET06	2	0	0	1	4	0	0	1	1	0	2	0	0	0	0	0	0	0	0
CmSWEET07	0	0	0	0	7	0	0	0	0	0	0	0	2	1	0	0	0	2	0
CmSWEET08	1	0	0	0	4	0	0	0	0	0	1	0	1	3	0	0	1	0	0
CmSWEET09	0	0	0	0	2	1	1	0	0	0	0	0	1	1	0	0	0	0	0
CmSWEET10	1	0	0	0	3	2	1	0	0	0	0	0	4	0	0	0	0	0	0
CmSWEET11	3	0	0	0	1	1	0	0	0	0	0	0	2	1	0	0	0	0	0
CmSWEET12	1	0	0	1	2	0	0	0	0	0	1	0	0	1	0	0	1	1	0
CmSWEET13	2	0	0	0	1	1	0	0	0	0	0	0	0	2	1	0	0	2	0
CmSWEET14	0	0	1	0	2	0	0	0	0	0	0	0	2	1	0	0	1	0	0
CmSWEET15	0	0	1	1	7	1	0	0	0	0	0	1	2	4	0	1	0	2	0
CmSWEET16	2	0	0	0	2	0	0	1	1	0	0	0	0	1	0	0	0	4	0
CmSWEET17	0	1	0	0	4	1	0	1	0	1	0	0	0	0	1	0	2	0	0

甜瓜SWEET基因家族的全基因组鉴定及生物信息学分析

Genome-wide identification and bioinformatics analysis of SWEET gene family in melon

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基因名称 Gene name	发育相关元件数量Number of development-related element
基因名称 Gene name	CAT-box	circadian	HD-Zip 1	MBSI	O2-site	GCN4_motif	RY-element
CmSWEET01	1	0	0	0	0	0	0
CmSWEET02	0	0	0	0	0	0	0
CmSWEET03	0	0	0	0	1	0	0
CmSWEET04	0	0	0	0	0	0	0
CmSWEET05	0	0	1	0	1	0	0
CmSWEET06	1	1	0	0	0	0	0
CmSWEET07	0	0	0	0	0	1	0
CmSWEET08	0	0	0	0	0	0	0
CmSWEET09	0	1	0	0	0	0	0
CmSWEET10	0	0	0	1	0	0	0
CmSWEET11	1	0	0	0	0	0	0
CmSWEET12	0	0	0	0	0	0	0
CmSWEET13	0	1	0	0	1	0	1
CmSWEET14	0	0	0	0	1	0	0
CmSWEET15	0	0	0	1	1	0	0
CmSWEET16	0	0	0	1	0	0	0
CmSWEET17	0	1	0	0	0	0	0

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