Journal of Nuclear Agricultural Sciences ›› 2022, Vol. 36 ›› Issue (2): 270-281.DOI: 10.11869/j.issn.100-8551.2022.02.0270
• Induced Mutations for Plant Breeding·Agricultural Biotechnology • Previous Articles Next Articles
ZHOU Shuqian1(), CHEN Lu1, CHEN Huiyun2, LI Yongxin1, CHEN Gang1, LU Guoquan1, YANG Huqing1,*(
)
Received:
2020-12-30
Accepted:
2021-02-08
Online:
2022-02-10
Published:
2022-01-17
Contact:
YANG Huqing
周淑倩1(), 陈璐1, 陈惠云2, 李永新1, 陈刚1, 陆国权1, 杨虎清1,*(
)
通讯作者:
杨虎清
作者简介:
周淑倩,女,主要从事农产品质量与安全控制研究。E-mail: 873306241@qq.com
基金资助:
ZHOU Shuqian, CHEN Lu, CHEN Huiyun, LI Yongxin, CHEN Gang, LU Guoquan, YANG Huqing. Bioinformatics and Expression Analysis of Alternative Oxidase Genes in Sweetpotato[J]. Journal of Nuclear Agricultural Sciences, 2022, 36(2): 270-281.
周淑倩, 陈璐, 陈惠云, 李永新, 陈刚, 陆国权, 杨虎清. 甘薯交替氧化酶基因家族生物信息学与表达分析[J]. 核农学报, 2022, 36(2): 270-281.
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URL: https://www.hnxb.org.cn/EN/10.11869/j.issn.100-8551.2022.02.0270
基因名称 Gene name | 引物序列(5'→3') Primer sequence(5'→3') | 产物大小 Product size/bp |
---|---|---|
IbAOX1a | F:ATGAGTCATAACGGGGCG R:CTAATGATACCCAATTGGAGCA | 963 |
IbAOX1b | F:ATGATGAGCCGTGGCG R:TTAGTGATATCCAAGAGGGGC | 1 080 |
IbAOX2 | F:ATGAATCAGTTGCTGGCTAG R:TCAGTGGTACCCAATAGGA | 1 040 |
Table 1 Full-length primers of AOX gene family in sweetpotato
基因名称 Gene name | 引物序列(5'→3') Primer sequence(5'→3') | 产物大小 Product size/bp |
---|---|---|
IbAOX1a | F:ATGAGTCATAACGGGGCG R:CTAATGATACCCAATTGGAGCA | 963 |
IbAOX1b | F:ATGATGAGCCGTGGCG R:TTAGTGATATCCAAGAGGGGC | 1 080 |
IbAOX2 | F:ATGAATCAGTTGCTGGCTAG R:TCAGTGGTACCCAATAGGA | 1 040 |
基因名称 Gene name | 引物序列(5'→3') Primer sequence(5'→3') | 产物大小 Product size/bp |
---|---|---|
IbAOX1a | F:TCCTGGAAGAAGCGGAGAAC R:GGTGAAGAAATAGGCGTTGAA | 128 |
IbAOX1b | F:AGTGCTGGTTGCTTGGATGA R:CCATTCCGTGCCATCCTCTT | 199 |
IbAOX2 | F:GTTGCCTCCAATGATTACCA R:AACTCTCGTGAATAGCCCTCA | 93 |
Table 2 qRT-PCR primers for AOX gene family in sweetpotato
基因名称 Gene name | 引物序列(5'→3') Primer sequence(5'→3') | 产物大小 Product size/bp |
---|---|---|
IbAOX1a | F:TCCTGGAAGAAGCGGAGAAC R:GGTGAAGAAATAGGCGTTGAA | 128 |
IbAOX1b | F:AGTGCTGGTTGCTTGGATGA R:CCATTCCGTGCCATCCTCTT | 199 |
IbAOX2 | F:GTTGCCTCCAATGATTACCA R:AACTCTCGTGAATAGCCCTCA | 93 |
Fig.1 PCR amplification of IbAOXs gene and pMD19-T-IbAOXs recombinant vector Note: A: M: Marker. 1: IbAOX1a. 2: IbAOX1b. 3: IbAOX2. B: M: Marker. 1: PMD19-T-IbAOX1a recombinant carrier bacterial solution.2: PMD19-T-IbAOX1b recombinant carrier bacterial solution. 3: PMD19-T-IbAOX2 recombinant carrier bacterial solution.
基因名称 Gene name | 编码区序 列长度 Coding sequence length/bp | 蛋白长度 Protein length/aa | 分子式 Formula | 分子量 Molecular weight/Da | 等电点 pI | 不稳定指数 Instability index | 脂溶指数 Aliphatic index | 总平均 亲水性 GRAVY | 亚细胞 定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
IbAOX1a | 963 | 320 | C1649H2500 N448O458S11 | 36 281.38 | 8.24 | 42.25 | 78.12 | -0.290 | 线粒体 |
IbAOX1b | 1 080 | 359 | C1815H2794 N508O507S16 | 40 356.21 | 8.79 | 43.75 | 75.29 | -0.292 | 线粒体 |
IbAOX2 | 1 032 | 343 | C1755H2751 N487O489S23 | 39 234.50 | 8.91 | 39.07 | 82.48 | -0.206 | 线粒体 |
Table 3 Basic physicochemical characteristics and subcellular localization prediction of AOX gene family in sweetpotato
基因名称 Gene name | 编码区序 列长度 Coding sequence length/bp | 蛋白长度 Protein length/aa | 分子式 Formula | 分子量 Molecular weight/Da | 等电点 pI | 不稳定指数 Instability index | 脂溶指数 Aliphatic index | 总平均 亲水性 GRAVY | 亚细胞 定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
IbAOX1a | 963 | 320 | C1649H2500 N448O458S11 | 36 281.38 | 8.24 | 42.25 | 78.12 | -0.290 | 线粒体 |
IbAOX1b | 1 080 | 359 | C1815H2794 N508O507S16 | 40 356.21 | 8.79 | 43.75 | 75.29 | -0.292 | 线粒体 |
IbAOX2 | 1 032 | 343 | C1755H2751 N487O489S23 | 39 234.50 | 8.91 | 39.07 | 82.48 | -0.206 | 线粒体 |
Fig.4 Multiple sequence alignment of AOX protein in sweetpotato Note: The color from dark to light represents 100%, 75%, 50% and less than 50% homology. IbAOXs: Ipomoea batatas (MT992313, MT992314, MG450566.1). AtAOXs: Arabidopsis thaliana (NP_188876.1, NP_188871.1, NP_189399.1, NP_564395.1, AAY78882.1). SlAOXs: Solanum lycopersicum(NP_001234117.2, NP_001234120.1, NP_001309890.1). DhAOX: Dorcoceras hygrometricum (KZV31497.1).
Motif | 长度 Length/bp | 蛋白保守序列 Protein conserved sequence |
---|---|---|
Motif1 | 50 | WKWNCFRPWETYKADVSIDLKKHHVPKTFMDKFAYWTVKALRFPTDIFFQ |
Motif2 | 50 | PGMVGGMLLHCKSLRRFEHSGGWIKALLEEAENERMHLMTFIELSKPRWY |
Motif3 | 50 | IENIPAPAIAIDYWRLPPDARLKDVITVIRADEAHHRDVNHFASDIRFQG |
Motif4 | 50 | LVFAVQGVFFNAYFVAYLASPKLAHRIVGYLEEEAIHSYTEFLNDIDNGK |
Motif5 | 15 | RRYGCRAMMLETVAA |
Motif6 | 18 | VSSYWGVDPPKVSKEDGS |
Motif7 | 11 | LKEAPAPIGYH |
Motif8 | 10 | ZKEKDEKNGG |
Motif9 | 7 | WLDEPVM |
Motif10 | 6 | PRIFSV |
Motif11 | 6 | SRRMMS |
Motif12 | 7 | MSRGCCR |
Motif13 | 6 | GEGGIG |
Motif14 | 6 | HGGPVK |
Motif15 | 10 | NQAAGEAVDR |
Motif16 | 6 | RRWATA |
Motif17 | 6 | SRYDSA |
Motif18 | 6 | RSLYGN |
Motif19 | 6 | ASEEKK |
Motif20 | 7 | SGTLLRK |
Table 4 Conserved sequence of AOX protein in sweetpotato
Motif | 长度 Length/bp | 蛋白保守序列 Protein conserved sequence |
---|---|---|
Motif1 | 50 | WKWNCFRPWETYKADVSIDLKKHHVPKTFMDKFAYWTVKALRFPTDIFFQ |
Motif2 | 50 | PGMVGGMLLHCKSLRRFEHSGGWIKALLEEAENERMHLMTFIELSKPRWY |
Motif3 | 50 | IENIPAPAIAIDYWRLPPDARLKDVITVIRADEAHHRDVNHFASDIRFQG |
Motif4 | 50 | LVFAVQGVFFNAYFVAYLASPKLAHRIVGYLEEEAIHSYTEFLNDIDNGK |
Motif5 | 15 | RRYGCRAMMLETVAA |
Motif6 | 18 | VSSYWGVDPPKVSKEDGS |
Motif7 | 11 | LKEAPAPIGYH |
Motif8 | 10 | ZKEKDEKNGG |
Motif9 | 7 | WLDEPVM |
Motif10 | 6 | PRIFSV |
Motif11 | 6 | SRRMMS |
Motif12 | 7 | MSRGCCR |
Motif13 | 6 | GEGGIG |
Motif14 | 6 | HGGPVK |
Motif15 | 10 | NQAAGEAVDR |
Motif16 | 6 | RRWATA |
Motif17 | 6 | SRYDSA |
Motif18 | 6 | RSLYGN |
Motif19 | 6 | ASEEKK |
Motif20 | 7 | SGTLLRK |
蛋白名称 Protein name | α-螺旋 Alpha helix | 延伸链 Extended strand | β-转角 Beta turn | 不规则卷曲 Random coil |
---|---|---|---|---|
IbAOX1a | 47.19 | 14.06 | 7.50 | 31.25 |
IbAOX1b | 46.80 | 12.53 | 5.85 | 34.82 |
IbAOX2 | 60.64 | 7.00 | 4.57 | 27.99 |
Table 5 Analysis of the secondary structure of AOX proteins in sweetpotato/%
蛋白名称 Protein name | α-螺旋 Alpha helix | 延伸链 Extended strand | β-转角 Beta turn | 不规则卷曲 Random coil |
---|---|---|---|---|
IbAOX1a | 47.19 | 14.06 | 7.50 | 31.25 |
IbAOX1b | 46.80 | 12.53 | 5.85 | 34.82 |
IbAOX2 | 60.64 | 7.00 | 4.57 | 27.99 |
Fig.8 Expression analysis of IbAOXs genes in tuberous roots, fibrous roots, stems, leaves and buds of sweetpotato Note: Different lowercase letters indicate significant differences at 0.05 level.
Fig.9 Analysis of IbAOXs gene expression in sweetpotato seedlings in response to low temperature drought and high salt stress Note: The difference between the two points is greater than LSD indicate significant differences at 0.05 level. The same as following.
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