龙眼SKP1-like家族成员鉴定及体胚发生早期表达分析

doi:10.16420/j.issn.0513-353x.2020-0636

摘要/Abstract

摘要：

为研究S-phase kinase-associated protein 1-like（SKP1-like）在龙眼中的分子特性以及其在体胚发生早期的表达模式,基于模式植物拟南芥SKP1-like的氨基酸序列,在龙眼基因组数据库中进行SKP1-like成员的鉴定。同时,通过生物信息学方法对其蛋白理化性质、系统进化特征、染色体定位、共线性与选择压力、基因结构、保守基序、蛋白结构、蛋白互作网络、启动子顺式元件进行分析,并结合龙眼转录组数据分析其在体胚发生早期的表达模式。研究结果表明：龙眼SKP1-like家族基因共有14个成员,分别将其命名为DlSKP1-1 ~ DlSKP1-14。龙眼SKP1-like（DlSKP1）家族基因编码蛋白质的氨基酸数、分子量以及等电点分别为75 ~ 399 aa、8.29 ~ 45.34 kD、4.44 ~ 5.76,均不含信号肽,可能主要定位于叶绿体中。DlSKP1家族存在1对串联重复基因以及4对片段重复基因。蛋白互作结果提示,DlSKP1家族成员可能与多种蛋白（尤其F-Box家族蛋白）存在互作关系。启动子顺式作用元件的结果表明,DlSKP1家族成员启动子含有较多脱落酸（Abscisic acid,ABA）与茉莉酸甲酯（Methyl jasmonate,MeJA）响应元件。此外,DlSKP1成员在龙眼体胚发生早期存在5种不同的表达模式,其中3个成员（DlSKP1-6、DlSKP1-8、DlSKP1-13）在各阶段的表达量较其他成员较高。研究结果显示,DlSKP1家族成员可能与F-Box蛋白存在互作作用,并且可能参与ABA、MeJA的调控过程,还可能在龙眼体胚的形态建成中发挥重要作用。

关键词: 龙眼, SKP1-like家族, 全基因组鉴定, 分子特性, 体胚发生早期, 表达模式

Abstract:

Based on the amino acid sequence of Arabidopsis SKP1-like,the SKP1-like members were identified in the longan genome database to explore the molecular characteristics and its expression patterns during early somatic embryogenesis in Dimocarpus longan. In the meanwhile,bioinformatics methods were used to analyse the physical and chemical properties of its protein,system evolution characteristics,chromosome positioning,collinearity and selective pressure,gene structure,conserved motifs,protein structure,protein interaction network,promoter cis-elements. The results showed that there were 14 SKP1-like family members in longan,which were named as DlSKP1-1-DlSKP1-14. The number of amino acids,molecular weight and isoelectric point of proteins encoded by the family genes were 75 to 399 aa,8.29 to 45.34 kD,and 4.44 to 5.76,respectively. They did not contain signal peptides and might be mainly located in chloroplast. There were one pair of tandem repeat genes and four pairs of fragment repeat genes in the DlSKP1 family. The protein interaction prediction results suggested that DlSKP1 family members might interact with multiple proteins（especially F-Box family proteins）. The results of the promoter cis-acting elements showed that the promoters of DlSKP1 family members contained more abscisic acid（ABA）and methyl jasmonate（MeJA）response elements. In addition,longan DlSKP1 members had five different expression patterns during early somatic embryogenesis,among which three members（DlSKP1-6,DlSKP1-8,DlSKP1-13）had higher expression levels than other members at each stage. The results of the study indicated that DlSKP1 family members might interact with the F-Box proteins,participate in the regulation of ABA and MeJA,and also play an important role in the morphogenesis of longan somatic embryos.

Key words: Dimocarpus longan, SKP1-like family, geome-wide identification, molecular characteristics, early somatic embryogenesis, expression

中图分类号:

S667.2

张春渝, 许小琼, 徐小萍, 赵鹏程, 申序, MunirNigarish, 张梓浩, 林玉玲, 陈振光, 赖钟雄. 龙眼SKP1-like家族成员鉴定及体胚发生早期表达分析[J]. 园艺学报, 2021, 48(9): 1665-1679.

ZHANG Chunyu, XU Xiaoqiong, XU Xiaoping, ZHAO Pengcheng, SHEN Xu, Munir Nigarish, ZHANG Zihao, LIN Yuling, Chen Zhenguang, LAI Zhongxiong. Genome-wide Identification of the SKP1-like Family and Analysis of Their Expression During Early Somatic Embryogenesis in Longan[J]. Acta Horticulturae Sinica, 2021, 48(9): 1665-1679.

图/表 7

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基因ID Gene ID	基因名 Gene name	基因位置 Location	氨基酸数 Number of amino acids	等电点 pI	分子量/kD Molecule weight	不稳定系数 Instability index	平均亲水性 Grand average of hydropathicity	亚细胞定位预测 Subcellular localization
Dlo004376	DlSKP1-1	Chr2:8659065:8659292:+	75	5.62	8.29	55.10	0.189	叶绿体Chloroplast
Dlo006336	DlSKP1-2	Chr3:3247223:3247714:-	163	4.51	18.34	40.04	-0.421	叶绿体Chloroplast
Dlo006338	DlSKP1-3	Chr3:3263169:3263666:-	165	4.81	18.88	48.13	-0.503	细胞质Cytoplasm
Dlo006553	DlSKP1-4	Chr3:5966103:5966600:+	165	4.45	18.64	50.31	-0.441	叶绿体Chloroplast
Dlo012745	DlSKP1-5	Chr5:31590465:31597118:+	345	5.54	39.60	44.69	-0.823	细胞核Nuclear
Dlo013346	DlSKP1-6	Chr6:1792674:1794424:-	158	4.59	17.83	41.09	-0.494	细胞质Cytoplasm
Dlo013634	DlSKP1-7	Chr6:4396612:4402101:-	147	4.83	16.40	44.76	-0.334	细胞核Nuclear
Dlo015478	DlSKP1-8	Chr7:1231833:1233731:-	209	5.12	23.37	44.46	-0.498	叶绿体Chloroplast
Dlo019333	DlSKP1-9	Chr9:805779:806249:-	156	4.44	17.93	34.47	-0.220	细胞质Cytoplasm
Dlo019334	DlSKP1-10	Chr9:812332:812819:-	124	4.62	14.46	53.90	-0.764	细胞质Cytoplasm
Dlo019594	DlSKP1-11	Chr9:4007573:4010954:+	399	5.76	45.34	56.04	-0.647	细胞质Cytoplasm
Dlo022243	DlSKP1-12	Chr10:12177605:12182053:+	172	5.15	19.43	40.72	-0.305	细胞核Nuclear
Dlo023134	DlSKP1-13	Chr11:1244155:1245940:-	176	4.52	20.16	52.48	-0.561	叶绿体Chloroplast
Dlo034799	DlSKP1-14	unanchor445_1_409426:233674:234129:-	182	4.96	20.68	49.36	-0.565	叶绿体Chloroplast

基因ID Gene ID	基因名 Gene name	基因位置 Location	氨基酸数 Number of amino acids	等电点 pI	分子量/kD Molecule weight	不稳定系数 Instability index	平均亲水性 Grand average of hydropathicity	亚细胞定位预测 Subcellular localization
Dlo004376	DlSKP1-1	Chr2:8659065:8659292:+	75	5.62	8.29	55.10	0.189	叶绿体Chloroplast
Dlo006336	DlSKP1-2	Chr3:3247223:3247714:-	163	4.51	18.34	40.04	-0.421	叶绿体Chloroplast
Dlo006338	DlSKP1-3	Chr3:3263169:3263666:-	165	4.81	18.88	48.13	-0.503	细胞质Cytoplasm
Dlo006553	DlSKP1-4	Chr3:5966103:5966600:+	165	4.45	18.64	50.31	-0.441	叶绿体Chloroplast
Dlo012745	DlSKP1-5	Chr5:31590465:31597118:+	345	5.54	39.60	44.69	-0.823	细胞核Nuclear
Dlo013346	DlSKP1-6	Chr6:1792674:1794424:-	158	4.59	17.83	41.09	-0.494	细胞质Cytoplasm
Dlo013634	DlSKP1-7	Chr6:4396612:4402101:-	147	4.83	16.40	44.76	-0.334	细胞核Nuclear
Dlo015478	DlSKP1-8	Chr7:1231833:1233731:-	209	5.12	23.37	44.46	-0.498	叶绿体Chloroplast
Dlo019333	DlSKP1-9	Chr9:805779:806249:-	156	4.44	17.93	34.47	-0.220	细胞质Cytoplasm
Dlo019334	DlSKP1-10	Chr9:812332:812819:-	124	4.62	14.46	53.90	-0.764	细胞质Cytoplasm
Dlo019594	DlSKP1-11	Chr9:4007573:4010954:+	399	5.76	45.34	56.04	-0.647	细胞质Cytoplasm
Dlo022243	DlSKP1-12	Chr10:12177605:12182053:+	172	5.15	19.43	40.72	-0.305	细胞核Nuclear
Dlo023134	DlSKP1-13	Chr11:1244155:1245940:-	176	4.52	20.16	52.48	-0.561	叶绿体Chloroplast
Dlo034799	DlSKP1-14	unanchor445_1_409426:233674:234129:-	182	4.96	20.68	49.36	-0.565	叶绿体Chloroplast

物种种类 Species	物种成员 Species member	龙眼成员 longan members	Ka	Ks	Ka/Ks
拟南芥 Arabidopsis thaliana	ASK1	DlSKP1-6	0.11	2.18	0.05
	ASK4	DlSKP1-6	0.22	—	—
	ASK20	DlSKP1-5	0.20	1.75	0.11
	ASK21	DlSKP1-5	0.18	1.43	0.12
水稻 Oryza sativa	Os09t0539500-01	DlSKP1-8	0.25	0.63	0.40
甜橙 Citrus sinensis	Cs9g17620.3	DlSKP1-11	0.09	0.61	0.15
	orange1.1t00374.1	DlSKP1-5	0.10	0.67	0.16
	orange1.1t00374.1	DlSKP1-11	0.19	2.17	0.09
	Cs8g02550.1	DlSKP1-13	0.14	1.26	0.11
	Cs8g02550.1	DlSKP1-6	0.12	1.89	0.06
	Cs8g02550.1	DlSKP1-8	0.21	1.75	0.12
	Cs3g26510.1	DlSKP1-13	0.14	3.07	0.05
	Cs3g26510.1	DlSKP1-6	0.03	0.82	0.03
	Cs3g26510.1	DlSKP1-8	0.17	1.04	0.16
	Cs1g25860.1	DlSKP1-13	0.23	1.76	0.13
	Cs1g25860.1	DlSKP1-6	0.11	1.47	0.07
	Cs1g25860.1	DlSKP1-8	0.23	0.94	0.25

物种种类 Species	物种成员 Species member	龙眼成员 longan members	Ka	Ks	Ka/Ks
拟南芥 Arabidopsis thaliana	ASK1	DlSKP1-6	0.11	2.18	0.05
	ASK4	DlSKP1-6	0.22	—	—
	ASK20	DlSKP1-5	0.20	1.75	0.11
	ASK21	DlSKP1-5	0.18	1.43	0.12
水稻 Oryza sativa	Os09t0539500-01	DlSKP1-8	0.25	0.63	0.40
甜橙 Citrus sinensis	Cs9g17620.3	DlSKP1-11	0.09	0.61	0.15
	orange1.1t00374.1	DlSKP1-5	0.10	0.67	0.16
	orange1.1t00374.1	DlSKP1-11	0.19	2.17	0.09
	Cs8g02550.1	DlSKP1-13	0.14	1.26	0.11
	Cs8g02550.1	DlSKP1-6	0.12	1.89	0.06
	Cs8g02550.1	DlSKP1-8	0.21	1.75	0.12
	Cs3g26510.1	DlSKP1-13	0.14	3.07	0.05
	Cs3g26510.1	DlSKP1-6	0.03	0.82	0.03
	Cs3g26510.1	DlSKP1-8	0.17	1.04	0.16
	Cs1g25860.1	DlSKP1-13	0.23	1.76	0.13
	Cs1g25860.1	DlSKP1-6	0.11	1.47	0.07
	Cs1g25860.1	DlSKP1-8	0.23	0.94	0.25

顺式作用元件种类 Kinds of cis-acting elements	DlSKP1-1	DlSKP1-2	DlSKP1-3	DlSKP1-4	DlSKP1-5	DlSKP1-6	DlSKP1-7
TATA-box	38	29	36	46	57	48	64
CAAT-box	35	34	41	37	43	52	28
光响应Light responsiveness	10	7	13	7	3	23	19
MYB结合情况下的光响应 MYB binding site involved in light responsiveness	0	0	1	1	0	0	0
MYB结合情况下的干旱胁迫 MYB binding site involved in drought inducibility	2	2	1	1	2	0	0
压力胁迫 Defense and stress	1	0	0	0	0	1	1
厌氧反应 Anaerobic response	4	1	3	1	1	3	2
缺氧诱导 Anoxic specific inducibility	0	1	1	0	1	0	1
低温 Low-temperature	0	4	0	1	1	0	0
机械损伤 Wound-responsive	0	0	0	0	0	0	0
赤霉素 Gibberellin	1	0	1	0	0	0	1
脱落酸 Abscisic acid	3	2	0	0	1	6	7
水杨酸 Salicylic acid	0	1	1	0	0	0	0
生长素 Auxin	0	0	2	0	1	0	0
茉莉酸甲酯 MeJA	0	0	0	2	0	2	4
胚乳 Endosperm	2	0	1	0	0	0	0
光敏色素下调 Phytochrome down-regulation	1	0	0	0	0	0	0
分生组织表达Meristem expression	0	1	0	0	0	0	1
细胞周期 Cell cycle regulation	0	0	1	0	0	0	0
昼夜节律调控 Circadian control	0	0	0	0	0	1	0
栅栏叶肉细胞的分化 Differentiation of the palisade mesophyll cells	0	0	0	0	0	1	0
种子特异调控 Seed-specific regulation	0	0	0	0	0	0	0
MYBHv1结合位点 MYBHv1 binding site	0	1	1	1	0	0	0
顺式作用元件种类 Kinds of cis-acting elements	DlSKP1-8	DlSKP1-9	DlSKP1-10	DlSKP1-11	DlSKP1-12	DlSKP1-13	DlSKP1-14
TATA-box	52	47	77	41	80	32	32
CAAT-box	33	46	58	45	40	66	53
光响应Light responsiveness	9	5	13	10	11	12	22
MYB结合情况下的光响应 MYB binding site involved in light responsiveness	1	0	0	1	0	1	0
MYB结合情况下的干旱胁迫 MYB binding site involved in drought inducibility	0	0	0	2	0	0	1
压力胁迫 Defense and stress	0	1	1	0	0	0	0
厌氧反应 Anaerobic response	2	3	1	4	4	6	3
缺氧诱导 Anoxic specific inducibility	0	0	0	0	0	0	1
低温 Low-temperature	0	1	0	0	1	0	0
机械损伤 Wound-responsive	0	0	0	1	0	0	0
赤霉素 Gibberellin	2	1	0	3	1	2	0
脱落酸 Abscisic acid	1	1	2	6	0	1	5
水杨酸 Salicylic acid	0	1	1	0	0	0	0
生长素 Auxin	0	1	0	1	0	1	0
茉莉酸甲酯 MeJA	0	0	0	6	2	2	2
胚乳 Endosperm	0	0	1	1	0	0	0
光敏色素下调 Phytochrome down-regulation	0	0	0	0	0	0	0
分生组织表达Meristem expression	3	0	0	3	1	1	1
细胞周期 Cell cycle regulation	0	0	0	0	0	2	0
昼夜节律调控 Circadian control	0	0	0	0	0	0	1
栅栏叶肉细胞的分化 Differentiation of the palisade mesophyll cells	0	0	0	0	0	0	1
种子特异调控 Seed-specific regulation	1	0	0	0	0	0	0
MYBHv1结合位点 MYBHv1 binding site	0	0	0	0	0	0	0