生物技术通报 ›› 2025, Vol. 41 ›› Issue (2): 221-233.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0704
• 研究报告 • 上一篇
匡健华1(), 程志鹏1, 赵永晶1, 杨洁1, 陈润乔2, 陈龙清1, 胡慧贞1(
)
收稿日期:
2024-07-21
出版日期:
2025-02-26
发布日期:
2025-02-28
通讯作者:
胡慧贞,女,博士,副研究员,研究方向 :园林植物与观赏园艺资源及应用;E-mail: Jenny_0129@swfu.edu.cn作者简介:
匡健华,男,硕士研究生,研究方向 :观赏植物资源及应用;E-mail: wyzdzjy_6-09@swfu.edu.cn
基金资助:
KUANG Jian-hua1(), CHENG Zhi-peng1, ZHAO Yong-jing1, YANG Jie1, CHEN Run-qiao2, CHEN Long-qing1, HU Hui-zhen1(
)
Received:
2024-07-21
Published:
2025-02-26
Online:
2025-02-28
摘要:
目的 探究荷花(Nelumbo nucifera)NnGH3家族成员的特征及其在非生物胁迫响应中的作用,为荷花抗逆新品种的选育提供新的关键候选基因资源。 方法 采用生物信息学方法从荷花全基因组中鉴定酰基酰胺合成酶(GH3)家族成员,对GH3基因编码的酰胺合成酶理化性质、染色体定位、三级结构预测、系统发育树、基因结构、共线性和表达模式等进行详细研究,并利用RT-qPCR技术探究NnGH3家族基因分别在低温(4℃)、厌氧(水淹)、盐害(300 mmol/L NaCl)及外源施加激素(0.1 mmol/L IAA、1 mmol/L JA和5 mmol/L SA)处理下的表达模式。 结果 从荷花基因组中鉴定出14个NnGH3家族成员,它们集中分布在5条染色体上,根据其在染色体的位置依次命名为NnGH3.1-3.14,其分子质量为365-630 aa,理论等电点均小于7,为酸性蛋白,亚细胞定位于细胞核和细胞质上;聚类分析表明GH3家族成员分为Group Ⅰ和Group Ⅱ两组,绝大多数成员含有3-4个外显子和GH3 superfamily结构域。14个NnGH3基因中有2对基因存在共线性,与拟南芥(Arabidopsis thaliana)、水稻(Oryza sativa)GH3基因分别存在14和6对共线关系。顺式作用元件预测分析表明,该家族基因存在大量光、逆境和激素等响应元件。表达分析结果显示,NnGH3负向响应低温胁迫,绝大多数成员正向响应SA处理和盐胁迫,特异性响应IAA、JA处理及厌氧胁迫,其中Group Ⅱ中的NnGH3.4和NnGH3.13基因以及Group Ⅰ中的NnGH3.3基因在所有处理中表达量变化最为显著。 结论 在全基因组范围内从荷花中系统鉴定得到14个NnGH3家族成员,分为Group Ⅰ和Group Ⅱ两组,均含有GH3 superfamily结构域,为酸性蛋白。NnGH3家族基因在不同的外源激素和非生物胁迫条件下的表达具有特异性。
匡健华, 程志鹏, 赵永晶, 杨洁, 陈润乔, 陈龙清, 胡慧贞. 激素和非生物胁迫下荷花GH3基因家族的表达分析[J]. 生物技术通报, 2025, 41(2): 221-233.
KUANG Jian-hua, CHENG Zhi-peng, ZHAO Yong-jing, YANG Jie, CHEN Run-qiao, CHEN Long-qing, HU Hui-zhen. Expression Analysis of the GH3 Gene Family in Nelumbo nucifera underHormonal and Abiotic Stresses[J]. Biotechnology Bulletin, 2025, 41(2): 221-233.
序号 No. | 基因名称 Gene name | 正向引物 Forward primer (5′-3′) | 反向引物 Reverse primer (5′-3′) |
---|---|---|---|
1 | NnGH3.1 | TCACTCAGTTCTGGCACCAC | TGCAAGACCCCCTTTCGTTT |
2 | NnGH3.2 | GGCAACCCATGACTACGTGA | CTGTACGCCCATTAAGCCCA |
3 | NnGH3.3 | GATGGTTCGAAGAGGTCGCA | GAGGTGTACAGGGCTTCCAG |
4 | NnGH3.4 | CTCACGCCTGTGATGAACCT | CTGGTCTTGAAGTGGTCGCT |
5 | NnGH3.5 | GGTTCGAAGAGGTGGCAGAA | AATCCGCATGGGAAGCAAGA |
6 | NnGH3.6 | AGCGCCCATGTCGAATACTT | GGGTAATCCGCAGAGGATGG |
7 | NnGH3.7 | CTAACGGGGAGGCATCAAGG | GACAGGCACCAGCAGGTTAT |
8 | NnGH3.8 | CCTGACTTCCGCCAATCCTT | CTAGTTCAGGGTTGGGCCTG |
9 | NnGH3.9 | GTCTGGACCAAGGGAAAGGG | CTCGCTGTACCAGACCACAA |
10 | NnGH3.10 | GTACAAAGGGGAGGAGGCAC | GACGCTTGAACGTTGTCACC |
11 | NnGH3.11 | ACTACGGAAGCTGGAGGACT | GGGCGTAGTCGTCGTAAGAG |
12 | NnGH3.12 | CCTCTTGCTTCCCATGCAGA | ACCCTTGATCTGTAAGCGGC |
13 | NnGH3.13 | AGTTCTGGAACTTCTGCGGG | ACCTGGCGTCTTTGTCTCTG |
14 | NnGH3.14 | AGCCCCCATATGATCGTTGC | GATCGGTTCTGACTCAGCGT |
15 | NnACT | CTCCGTGTTGCCCCTGAAG | CCAGCAAGGTCCAACCGAAG |
表1 引物序列表
Table 1 Sequences of primers
序号 No. | 基因名称 Gene name | 正向引物 Forward primer (5′-3′) | 反向引物 Reverse primer (5′-3′) |
---|---|---|---|
1 | NnGH3.1 | TCACTCAGTTCTGGCACCAC | TGCAAGACCCCCTTTCGTTT |
2 | NnGH3.2 | GGCAACCCATGACTACGTGA | CTGTACGCCCATTAAGCCCA |
3 | NnGH3.3 | GATGGTTCGAAGAGGTCGCA | GAGGTGTACAGGGCTTCCAG |
4 | NnGH3.4 | CTCACGCCTGTGATGAACCT | CTGGTCTTGAAGTGGTCGCT |
5 | NnGH3.5 | GGTTCGAAGAGGTGGCAGAA | AATCCGCATGGGAAGCAAGA |
6 | NnGH3.6 | AGCGCCCATGTCGAATACTT | GGGTAATCCGCAGAGGATGG |
7 | NnGH3.7 | CTAACGGGGAGGCATCAAGG | GACAGGCACCAGCAGGTTAT |
8 | NnGH3.8 | CCTGACTTCCGCCAATCCTT | CTAGTTCAGGGTTGGGCCTG |
9 | NnGH3.9 | GTCTGGACCAAGGGAAAGGG | CTCGCTGTACCAGACCACAA |
10 | NnGH3.10 | GTACAAAGGGGAGGAGGCAC | GACGCTTGAACGTTGTCACC |
11 | NnGH3.11 | ACTACGGAAGCTGGAGGACT | GGGCGTAGTCGTCGTAAGAG |
12 | NnGH3.12 | CCTCTTGCTTCCCATGCAGA | ACCCTTGATCTGTAAGCGGC |
13 | NnGH3.13 | AGTTCTGGAACTTCTGCGGG | ACCTGGCGTCTTTGTCTCTG |
14 | NnGH3.14 | AGCCCCCATATGATCGTTGC | GATCGGTTCTGACTCAGCGT |
15 | NnACT | CTCCGTGTTGCCCCTGAAG | CCAGCAAGGTCCAACCGAAG |
基因名称 Gene name | 基因ID Gene identifier | 氨基酸数目 Amino acid amount | α螺旋 Alpha helix (Hh)/% | 无规则卷曲Random coil (Cc)/% | 延伸链 Extended strand (Ee)/% | β折叠 Beta turn (Tt)/% | 跨膜结构域数目 Transmembrane domain number | 信号肽数 Signal peptides |
---|---|---|---|---|---|---|---|---|
NnGH3.1 | Nn1g01814.2 | 586 | 34.64 | 57.85 | 7.51 | 0.00 | 0 | 0 |
NnGH3.2 | Nn1g03776.1 | 621 | 34.14 | 60.39 | 5.48 | 0.00 | 0 | 0 |
NnGH3.3 | Nn1g03969.3 | 590 | 32.88 | 59.49 | 7.63 | 0.00 | 0 | 0 |
NnGH3.4 | Nn1g04653.2 | 599 | 36.06 | 58.76 | 5.18 | 0.00 | 0 | 0 |
NnGH3.5 | Nn1g06683.3 | 595 | 34.62 | 55.63 | 9.75 | 0.00 | 0 | 0 |
NnGH3.6 | Nn1g06894.2 | 616 | 36.04 | 59.25 | 4.71 | 0.00 | 0 | 0 |
NnGH3.7 | Nn3g16244.1 | 630 | 40.48 | 54.60 | 4.92 | 0.00 | 0 | 0 |
NnGH3.8 | Nn3g19075.2 | 587 | 34.58 | 57.24 | 8.18 | 0.00 | 0 | 0 |
NnGH3.9 | Nn4g22107.1 | 615 | 36.91 | 57.24 | 5.85 | 0.00 | 0 | 0 |
NnGH3.10 | Nn4g25867.1 | 603 | 36.15 | 58.71 | 5.14 | 0.00 | 0 | 0 |
NnGH3.11 | Nn4g26117.1 | 579 | 38.51 | 53.71 | 7.77 | 0.00 | 0 | 0 |
NnGH3.12 | Nn5g29859.2 | 592 | 29.73 | 59.63 | 10.64 | 0.00 | 0 | 0 |
NnGH3.13 | Nn5g30464.6 | 595 | 34.45 | 60.84 | 4.71 | 0.00 | 0 | 0 |
NnGH3.14 | Nn7g36856.1 | 365 | 22.78 | 58.89 | 18.33 | 0.00 | 0 | 0 |
表2 荷花NnGH3基因家族二级结构预测
Table 2 Prediction of secondary structure of N. nuciferaNnGH3 gene family
基因名称 Gene name | 基因ID Gene identifier | 氨基酸数目 Amino acid amount | α螺旋 Alpha helix (Hh)/% | 无规则卷曲Random coil (Cc)/% | 延伸链 Extended strand (Ee)/% | β折叠 Beta turn (Tt)/% | 跨膜结构域数目 Transmembrane domain number | 信号肽数 Signal peptides |
---|---|---|---|---|---|---|---|---|
NnGH3.1 | Nn1g01814.2 | 586 | 34.64 | 57.85 | 7.51 | 0.00 | 0 | 0 |
NnGH3.2 | Nn1g03776.1 | 621 | 34.14 | 60.39 | 5.48 | 0.00 | 0 | 0 |
NnGH3.3 | Nn1g03969.3 | 590 | 32.88 | 59.49 | 7.63 | 0.00 | 0 | 0 |
NnGH3.4 | Nn1g04653.2 | 599 | 36.06 | 58.76 | 5.18 | 0.00 | 0 | 0 |
NnGH3.5 | Nn1g06683.3 | 595 | 34.62 | 55.63 | 9.75 | 0.00 | 0 | 0 |
NnGH3.6 | Nn1g06894.2 | 616 | 36.04 | 59.25 | 4.71 | 0.00 | 0 | 0 |
NnGH3.7 | Nn3g16244.1 | 630 | 40.48 | 54.60 | 4.92 | 0.00 | 0 | 0 |
NnGH3.8 | Nn3g19075.2 | 587 | 34.58 | 57.24 | 8.18 | 0.00 | 0 | 0 |
NnGH3.9 | Nn4g22107.1 | 615 | 36.91 | 57.24 | 5.85 | 0.00 | 0 | 0 |
NnGH3.10 | Nn4g25867.1 | 603 | 36.15 | 58.71 | 5.14 | 0.00 | 0 | 0 |
NnGH3.11 | Nn4g26117.1 | 579 | 38.51 | 53.71 | 7.77 | 0.00 | 0 | 0 |
NnGH3.12 | Nn5g29859.2 | 592 | 29.73 | 59.63 | 10.64 | 0.00 | 0 | 0 |
NnGH3.13 | Nn5g30464.6 | 595 | 34.45 | 60.84 | 4.71 | 0.00 | 0 | 0 |
NnGH3.14 | Nn7g36856.1 | 365 | 22.78 | 58.89 | 18.33 | 0.00 | 0 | 0 |
图3 荷花(14个)、拟南芥(19个)和水稻(13个)GH3 基因家族系统发育树代表NnGH3s:荷花;代表AtGH3s:拟南芥;代表OsGH3s:水稻
Fig. 3 Unrooted phylogenetic tree of the GH3 gene family in N. nucifera(14), A. thaliana(19) and O. sativa(13)indicates NnGH3s: Nelumbo nucifera; indicates AtGH3s: Arabidopsis thaliana; indicates OsGH3s: Oryza sativa
图5 NnGH3家族的种内共线性分析(A)和荷花、拟南芥、水稻的种间共线性分析(B)Chr1-Chr8代表荷花1-8号染色体,热图代表基因密度,红线条代表NnGH3基因的组内及种间共线性基因对
Fig. 5 Intraspecific covariance analysis of the NnGH3 family (A) and interspecific covariance analysis (B) of N. nucifera, A. thaliana, and O. sativaChr1-Chr8 indicate chromosome 1-8 of N. nucifera, the heat map indicates gene density, red lines indicate intragroup and interspecies covariate gene pairs for the NnGH3 gene
基因对 Gene pair | 非同义替换率 Non-synonymous substitution rate (Ka) | 同义替换率 Synonymous substitution rate (Ks) | Ka/Ks |
---|---|---|---|
NnGH3.1/NnGH3.8 | 0.082 | 0.651 | 0.126 |
NnGH3.4/NnGH3.13 | 0.043 | 0.523 | 0.081 |
表3 荷花 GH3 基因家族共线基因对的 Ka/Ks 值
Table 3 Ka/Ks values of collinear gene pairs of GH3 gene family in N. nucifera
基因对 Gene pair | 非同义替换率 Non-synonymous substitution rate (Ka) | 同义替换率 Synonymous substitution rate (Ks) | Ka/Ks |
---|---|---|---|
NnGH3.1/NnGH3.8 | 0.082 | 0.651 | 0.126 |
NnGH3.4/NnGH3.13 | 0.043 | 0.523 | 0.081 |
图 7 荷花在外源0.1 mmol/L IAA、5 mmol/L SA、1 mmol/L JA及低温(4℃)、水淹、300 mmol/L NaCl处理6 h后NnGH3家族基因的表达分析*:P<0.05,**:P<0.01表示基因的表达量与对照间差异显著
Fig. 7 Expression analysis of the NnGH3 gene family in N. nucifera treated with exogenous 0.1 mmol/L IAA, 5 mmol/L SA, 1 mmol/L JA, and (4℃) low temperature, flooding, 300 mmol/L NaCl for 6 h* P<0.05, **: P<0.01, indicates that the expression of the gene is significantly different from the control
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