Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (9): 1665-1679.doi: 10.16420/j.issn.0513-353x.2020-0636
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ZHANG Chunyu, XU Xiaoqiong, XU Xiaoping, ZHAO Pengcheng, SHEN Xu, Munir Nigarish, ZHANG Zihao, LIN Yuling, Chen Zhenguang, LAI Zhongxiong*()
Received:
2021-02-09
Revised:
2021-08-11
Online:
2021-09-25
Published:
2021-09-30
Contact:
LAI Zhongxiong
E-mail:Laizx01@163.com
CLC Number:
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.
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URL: https://www.ahs.ac.cn/EN/10.16420/j.issn.0513-353x.2020-0636
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 |
Table 1 Analysis of the basic physical and chemical properties of DlSKP1 family proteins
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 |
Fig. 2 Phylogenetic tree of the SKP1-like family members:longan,Arabidopsis,sweet orange,papaya,rice,grape,and apple The numbers are bootstrap values based on 1 000 iterations.
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 |
Table 2 Evolutionary selection pressure analysis of SKP1-like family collinear members in longan and Arabidopsis,longan and rice,and longan and sweet orange
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 |
Table 3 Analysis of cis-acting elements of the DlSKP1 gene family
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 |
Fig. 4 Analysis of specific expressions of DlSKP1 family members at different stages of early embryogenesis The values in the figure indicate the FPKM values of DlSKP1 members during early somatic embryogenesis.
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