园艺学报 ›› 2021, Vol. 48 ›› Issue (2): 205-218.doi: 10.16420/j.issn.0513-353x.2020-0272
• 研究论文 • 下一篇
杨亚明, 丁毓端, 陈丽娟, 田雪婷, 殷伟杰, 彭红慧, 杜薇, 梁丽平, 任小林*()
收稿日期:
2020-09-07
修回日期:
2020-11-11
出版日期:
2021-02-25
发布日期:
2021-03-09
通讯作者:
任小林
E-mail:renxl@nwsuaf.edu.cn
基金资助:
YANG Yaming, DING Yuduan, CHEN Lijuan, TIAN Xueting, YIN Weijie, PENG Honghui, DU Wei, LIANG Liping, REN Xiaolin*()
Received:
2020-09-07
Revised:
2020-11-11
Online:
2021-02-25
Published:
2021-03-09
Contact:
REN Xiaolin
E-mail:renxl@nwsuaf.edu.cn
摘要:
液泡铁离子转运蛋白(vacuolar iron transporter,VIT)参与铁的储存和运输,对植物光合作用、固氮、呼吸、DNA和激素合成有重要作用。本研究中鉴定了苹果全基因组的9个VIT基因,通过系统发育分析其进化关系,表明苹果VIT蛋白与拟南芥进化关系较近。染色体定位显示9个VIT基因分布在7条染色体上,VIT基因的启动子区域富含光反应、植物激素调控和启动子相关顺式作用元件。表达谱分析显示VIT基因在花和果实中的表达量相对较高。此外,对MdVIT家族进行蛋白理化性质、String互作网络和基因结构等分析,表明苹果VIT家族扩增的主要因素是串联重复和片段复制,与苹果VIT蛋白互作的主要蛋白是阳离子共转运蛋白(XP_008372221.1和XP_008383418.1)。qRT-PCR分析结果表明:在2 000 μmol · L-1 FeSO4 · 7H2O(高铁)处理的‘M26’苹果砧木苗中,苹果VIT家族基因在不同组织的表达中存在差异,6 h后,MdVIT4在茎中的相对表达量最高,是对照的237倍。24 h后,MdVIT1和MdVIT2在叶片中的相对表达量与对照相比呈现上调表达,分别是对照的6.6倍和12.0倍。综上,基因MdVIT1、MdVIT2和MdVIT4可能与植物耐铁胁迫有密切关系,为苹果逆境胁迫机制研究提供参考。
中图分类号:
杨亚明, 丁毓端, 陈丽娟, 田雪婷, 殷伟杰, 彭红慧, 杜薇, 梁丽平, 任小林. 苹果液泡铁离子转运蛋白基因家族的鉴定与表达分析[J]. 园艺学报, 2021, 48(2): 205-218.
YANG Yaming, DING Yuduan, CHEN Lijuan, TIAN Xueting, YIN Weijie, PENG Honghui, DU Wei, LIANG Liping, REN Xiaolin. Identification and Expression Analysis of the Vacuolar Iron Transporter Gene Family in Apple[J]. Acta Horticulturae Sinica, 2021, 48(2): 205-218.
用途Usage | 基因Gene | 上游引物(5′-3′)Forward primer | 下游引物(5′-3′)Reverse primer |
---|---|---|---|
qRT-PCR | MdVIT1 | CTCCAATCCCCGAAGACGA | GCGATGCAACGGAAACCA |
MdVIT2 | TCCGCTTCTCCCGTTAATATT | CGAGGTCGTTTGTGGTCATT | |
MdVIT3 | CACCAAACAACGCTAGACCAA | TCACAGCTCCGACTCCCAT | |
MdVIT4 | TTCGATTACTCCCAGAGGACAC | AGCGATGCAACAGAAACCAG | |
MdVIT5 | AATCCCAGAAGGCGACGAA | GAGCGATGCAACAGAAACCAGCCCA | |
MdVIT6 | TCTTACCGTGCCGTTTGCT | ATATCCGCCGAGTCCCATG | |
MdVIT7 | CAAGGACCGAGCAAGTGCA | CATCAAGGACGTGGTTGACAGT | |
MdVIT8 | CGACGGTCTCACTGTCCCTT | GGCGGCAACTTCAGCAAT | |
MdVIT9 | ACCGCGAGAAGCAAGCACT | AGCGAACGGCACGGTAAGA | |
克隆基因及 启动子 Clone primers | MD04G1208900 | ATGGCTTCCCAACGTGACCA | TCAGATTCCCAAACCACTAGACC |
MD05G1023100 | ATGTGTCCTCCACACTTCTCCAA | TCATAGCCCACTTGAGCCAATC | |
MD12G1223300 | ATGGCTTCCCAACGTGACCA | TCACACCTGCATACCACTAGAC |
表1 苹果VIT基因家族表达分析的实时荧光定量和克隆引物
Table 1 qRT-PCR and clone primers for expression on analysis of VIT in apple
用途Usage | 基因Gene | 上游引物(5′-3′)Forward primer | 下游引物(5′-3′)Reverse primer |
---|---|---|---|
qRT-PCR | MdVIT1 | CTCCAATCCCCGAAGACGA | GCGATGCAACGGAAACCA |
MdVIT2 | TCCGCTTCTCCCGTTAATATT | CGAGGTCGTTTGTGGTCATT | |
MdVIT3 | CACCAAACAACGCTAGACCAA | TCACAGCTCCGACTCCCAT | |
MdVIT4 | TTCGATTACTCCCAGAGGACAC | AGCGATGCAACAGAAACCAG | |
MdVIT5 | AATCCCAGAAGGCGACGAA | GAGCGATGCAACAGAAACCAGCCCA | |
MdVIT6 | TCTTACCGTGCCGTTTGCT | ATATCCGCCGAGTCCCATG | |
MdVIT7 | CAAGGACCGAGCAAGTGCA | CATCAAGGACGTGGTTGACAGT | |
MdVIT8 | CGACGGTCTCACTGTCCCTT | GGCGGCAACTTCAGCAAT | |
MdVIT9 | ACCGCGAGAAGCAAGCACT | AGCGAACGGCACGGTAAGA | |
克隆基因及 启动子 Clone primers | MD04G1208900 | ATGGCTTCCCAACGTGACCA | TCAGATTCCCAAACCACTAGACC |
MD05G1023100 | ATGTGTCCTCCACACTTCTCCAA | TCATAGCCCACTTGAGCCAATC | |
MD12G1223300 | ATGGCTTCCCAACGTGACCA | TCACACCTGCATACCACTAGAC |
基因名 Gene name | 登录号 Gene ID | 序列位置 Sequence position | 染色体 位置 Chr | 开放阅 读区/bp ORF | 氨基酸 数/aa Length of amino acid | 分子量/ kD Molecular weigh | 不稳定 系数 Instability index | 理论等 电点 pI | 蛋白质 疏水性 Hydroph- obicity | 脂肪指数 Aliphatic index | 跨膜结 构域 TMD |
---|---|---|---|---|---|---|---|---|---|---|---|
MdVIT1 | MD04G1208900 | 29415642..29416325 | Chr04 | 684 | 227 | 23.71 | 42.66 | 6.13 | 0.29 | 97.14 | 4 |
MdVIT2 | MD05G1023100 | 3872852..3873643 | Chr05 | 792 | 263 | 27.68 | 41.63 | 6.96 | 0.25 | 97.91 | 5 |
MdVIT3 | MD10G1024000 | 3007772..3008458 | Chr10 | 687 | 228 | 24.01 | 34.11 | 6.13 | 0.28 | 101.05 | 4 |
MdVIT4 | MD12G1223300 | 30004855..30005538 | Chr12 | 684 | 227 | 23.87 | 43.44 | 7.78 | 0.30 | 96.26 | 4 |
MdVIT5 | MD12G1223400 | 30015123..30015806 | Chr12 | 684 | 227 | 23.90 | 45.02 | 6.30 | 0.28 | 96.26 | 4 |
MdVIT6 | MD13G1018700 | 1174829..1178506 | Chr13 | 744 | 247 | 26.36 | 36.99 | 5.18 | 0.19 | 101.30 | 4 |
MdVIT7 | MD15G1227000 | 18449646..18451051 | Chr15 | 798 | 265 | 27.99 | 42.77 | 8.34 | 0.01 | 89.51 | 5 |
MdVIT8 | MD16G1016500 | 1240143..1242202 | Chr16 | 747 | 248 | 26.52 | 36.31 | 5.00 | 0.38 | 105.16 | 4 |
MdVIT9 | MD16G1016600 | 1243044..1245822 | Chr16 | 744 | 247 | 26.41 | 35.57 | 5.89 | 0.21 | 105.63 | 4 |
表2 苹果中VIT基因的基本信息
Table 2 Detailed information of identified VIT genes in apple genome
基因名 Gene name | 登录号 Gene ID | 序列位置 Sequence position | 染色体 位置 Chr | 开放阅 读区/bp ORF | 氨基酸 数/aa Length of amino acid | 分子量/ kD Molecular weigh | 不稳定 系数 Instability index | 理论等 电点 pI | 蛋白质 疏水性 Hydroph- obicity | 脂肪指数 Aliphatic index | 跨膜结 构域 TMD |
---|---|---|---|---|---|---|---|---|---|---|---|
MdVIT1 | MD04G1208900 | 29415642..29416325 | Chr04 | 684 | 227 | 23.71 | 42.66 | 6.13 | 0.29 | 97.14 | 4 |
MdVIT2 | MD05G1023100 | 3872852..3873643 | Chr05 | 792 | 263 | 27.68 | 41.63 | 6.96 | 0.25 | 97.91 | 5 |
MdVIT3 | MD10G1024000 | 3007772..3008458 | Chr10 | 687 | 228 | 24.01 | 34.11 | 6.13 | 0.28 | 101.05 | 4 |
MdVIT4 | MD12G1223300 | 30004855..30005538 | Chr12 | 684 | 227 | 23.87 | 43.44 | 7.78 | 0.30 | 96.26 | 4 |
MdVIT5 | MD12G1223400 | 30015123..30015806 | Chr12 | 684 | 227 | 23.90 | 45.02 | 6.30 | 0.28 | 96.26 | 4 |
MdVIT6 | MD13G1018700 | 1174829..1178506 | Chr13 | 744 | 247 | 26.36 | 36.99 | 5.18 | 0.19 | 101.30 | 4 |
MdVIT7 | MD15G1227000 | 18449646..18451051 | Chr15 | 798 | 265 | 27.99 | 42.77 | 8.34 | 0.01 | 89.51 | 5 |
MdVIT8 | MD16G1016500 | 1240143..1242202 | Chr16 | 747 | 248 | 26.52 | 36.31 | 5.00 | 0.38 | 105.16 | 4 |
MdVIT9 | MD16G1016600 | 1243044..1245822 | Chr16 | 744 | 247 | 26.41 | 35.57 | 5.89 | 0.21 | 105.63 | 4 |
蛋白 | 液泡 | 质膜 | 内质网 | 高尔基体 | 胞外 |
---|---|---|---|---|---|
Protein | Vacuolar | Plasma membrane | Endoplasmic reticulum | Golgi apparatus | Extracellular |
MdVIT1 | 9 | 4 | 1 | ||
MdVIT2 | 2 | 7 | 1 | ||
MdVIT3 | 12 | 2 | |||
MdVIT4 | 4 | 5.5 | 1 | 2 | |
MdVIT5 | 7 | 5 | 1 | 1 | |
MdVIT6 | 1 | 12 | |||
MdVIT7 | 2 | 5 | 6 | 1 | |
MdVIT8 | 2 | 8 | 3 | 1 | |
MdVIT9 | 2 | 12 |
表3 苹果MdVIT亚细胞定位预测
Table 3 Subcellular predication of apple MdVIT
蛋白 | 液泡 | 质膜 | 内质网 | 高尔基体 | 胞外 |
---|---|---|---|---|---|
Protein | Vacuolar | Plasma membrane | Endoplasmic reticulum | Golgi apparatus | Extracellular |
MdVIT1 | 9 | 4 | 1 | ||
MdVIT2 | 2 | 7 | 1 | ||
MdVIT3 | 12 | 2 | |||
MdVIT4 | 4 | 5.5 | 1 | 2 | |
MdVIT5 | 7 | 5 | 1 | 1 | |
MdVIT6 | 1 | 12 | |||
MdVIT7 | 2 | 5 | 6 | 1 | |
MdVIT8 | 2 | 8 | 3 | 1 | |
MdVIT9 | 2 | 12 |
图1 MdVIT家族系统发育树(A)基因的结构分析(B)和MdVIT蛋白的保守基序(C)
Fig. 1 Phylogenetic classification of MdVIT(A),gene structure analyses of MdVIT(B)and conserved motif of MdVIT proteins(C)
图2 拟南芥(At)、水稻(Os)、玉米(Zm)、葡萄(Vv)和苹果(Md)VIT 基因家族发育树
Fig. 2 The phylogenetic tree of VIT gene family in Arabidopsis thaliana(At),Oryza sativa(Os),Zea mays(Zm), Vitis vinifera(Vv)and Malus × domestica(Md)
基因 Gene | 基因 Gene | 同义 替换率 Ka | 非同义 替换率 Ks | 选择性 压力 Ka/Ks | 分离时间/Mya Divergence Time | 复制类型 Duplication Types |
---|---|---|---|---|---|---|
MdVIT1(MD04G1208900) | MdVIT5(MD12G1223400) | 0.055 | 0.226 | 0.245 | 7.527 | 片段复制 Segmental duplication |
MdVIT1(MD04G1208900) | MdVIT4(MD12G1223300) | 0.071 | 0.190 | 0.371 | 6.347 | 片段复制 Segmental duplication |
MdVIT2(MD05G1023100) | MdVIT3(MD10G1024000) | 1.030 | 0.912 | 1.130 | 30.387 | 串联重复 Tandem dupication |
MdVIT4(MD12G1223300) | MdVIT5(MD12G1223400) | 0.036 | 0.103 | 0.349 | 3.425 | 片段复制 Segmental duplication |
表4 苹果VIT串联重复基因的分离时间
Table 4 Divergence time of the VIT paralogues in apple
基因 Gene | 基因 Gene | 同义 替换率 Ka | 非同义 替换率 Ks | 选择性 压力 Ka/Ks | 分离时间/Mya Divergence Time | 复制类型 Duplication Types |
---|---|---|---|---|---|---|
MdVIT1(MD04G1208900) | MdVIT5(MD12G1223400) | 0.055 | 0.226 | 0.245 | 7.527 | 片段复制 Segmental duplication |
MdVIT1(MD04G1208900) | MdVIT4(MD12G1223300) | 0.071 | 0.190 | 0.371 | 6.347 | 片段复制 Segmental duplication |
MdVIT2(MD05G1023100) | MdVIT3(MD10G1024000) | 1.030 | 0.912 | 1.130 | 30.387 | 串联重复 Tandem dupication |
MdVIT4(MD12G1223300) | MdVIT5(MD12G1223400) | 0.036 | 0.103 | 0.349 | 3.425 | 片段复制 Segmental duplication |
图4 苹果MdVIT复制基因的染色体定位和共线性分析 红色线条表示1对复制基因。
Fig. 4 Chromosome location and collinear distribution of MdVIT genes in apple genome Red lines showed gene duplication.
图5 苹果与拟南芥的VIT基因的同源性分析 灰色线条代表苹果和拟南芥基因组中的共线性区域,红色线条突出显示了共线性VIT基因对。
Fig. 5 Synteny analysis of VIT genes between apple and Arabidopsis thaliana Gray lines in the background indicate the collinear blocks with apple and Arabidopsis thaliana,while the red lines highlight the syntenic VIT gene pairs.
图7 MdVIT在不同苹果种质的不同组织中的表达模式 GD表示‘金冠’;M69、M74、M20、X8877、M14、M49、X4102、X4442 × X2596和X3069 × X992为不同苹果杂交种。
Fig. 7 Expression profiles of MdVIT genes in different tissues and different apple varieties GD reference‘Golden Delicious’;M69,M74,M20,X8877,M14,M49,X4102,X4442 × X2596,and X3069 × X992 were various apple hybrids.
图8 MdVIT在苹果不同组织中的表达分析 处理与对照的差异显著性分析用t-test法统计。* α = 0.05,** α = 0.01.
Fig. 8 Expression profile of MdVIT in different tissues in apple Significance difference between treatment and the control were analyzed by t-test. * α = 0.05,** α = 0.01.
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