蛇足石杉YUCCA基因家族的生物信息学及其组织特异表达分析

doi:10.13304/j.nykjdb.2024.0297

摘要/Abstract

摘要：

YUCCA 基因编码黄素单加氧酶，在植物生长发育过程中起重要调控作用。为探究YUCCA 基因对蛇足石杉生长发育的作用，对蛇足石杉YUCCA 基因家族进行生物信息学及组织特异性表达分析。结果表明，在蛇足石杉全长转录组中共鉴定出 18个 HsYUCCA 基因家族成员，氨基酸长度为150~544 aa，蛋白质相对分子量为16 105.53~59 058.24 Da，等电点在4.36~9.63，其中，有9个为碱性蛋白，有4个为稳定蛋白，有15个为亲水蛋白，有7个具有跨膜结构，分布在细胞核、细胞膜、细胞质、线粒体、叶绿体以及过氧化物酶体中。HsYUCCA4 在孢子、茎、芽胞中的表达量最高，HsYUCCA6在叶中的表达量最高。HsYUCCA 启动子区拥有激素响应、光响应、胁迫响应等35种顺式作用元件，并具有15 种保守基序。HsYUCCA1、HsYUCCA2和HsYUCCA4，HsYUCCA5和HsYUCCA6，HsYUCCA7和HsYUCCA13具有相似的理化性质、亚细胞定位、二级结构、三级结构及保守基序，系统发育表现出一定的同源性，进化过程趋于一致。以上研究结果为解析蛇足石杉 YUCCA 基因在生长发育和繁殖过程中的作用机理提供了理论依据。

关键词: 蛇足石杉, YUCCA基因家族, 生物信息学, 表达分析

Abstract:

The YUCCA gene encodes flavin monooxygenase， which plays an important regulatory role in plant growth and development. In order to explore the effect of YUCCA gene on the growth and development of Huperzia serrata， bioinformatics and tissue-specific expression analysis of YUCCA gene family of H. serrata were carried out. The results showed that 18 members of the HsYUCCA gene family were identified in the full-length transcriptome of H. serrata. The amino acid length was 150~544 aa， the relative molecular weight of the protein was 16 105.53~59 058.24 Da， and the isoelectric point was 4.36~9.63. Among them， there were 9 basic proteins， 4 stable proteins， 15 hydrophilic proteins， and 7 proteins with transmembrane structure. The subcellular localization ofHsYUCCA were in the nucleus， cell membrane， cytoplasm， mitochondria， chloroplast and peroxisome. The expression of HsYUCCA4 was the highest in spores， stems and spores， and the expression of HsYUCCA6 was the highest in leaves. HsYUCCA had 35 cis-acting elements such as hormone response， light response and stress response， and had 15 conserved motifs. The physical and chemical properties， subcellular localization， secondary structure， tertiary structure and conserved motifs of HsYUCCA1， HsYUCCA2 and HsYUCCA4， HsYUCCA5 and HsYUCCA6， HsYUCCA7 and HsYUCCA13 were similar， indicating that their biological functions were similar， and the phylogenetic development showed certain homology， and the evolutionary process tended to be consistent. Above results provided a theoretical basis for the future analysis of the possible mechanism of YUCCA gene in the growth， development and reproduction of H. serrata.

Key words: Huperzia serrata, YUCCA gene family, bioinformatics, expression analysis

中图分类号:

S567

陈秋洁, 黄玉妹, 冼金燕, 李凯童, 黄杰兰, 石小秀, 王柳萍, 涂冬萍. 蛇足石杉YUCCA基因家族的生物信息学及其组织特异表达分析[J]. 中国农业科技导报, 2025, 27(10): 72-83.

Qiujie CHEN, Yumei HUANG, Jinyan XIAN, Kaitong LI, Jielan HUANG, Xiaoxiu SHI, Liuping WANG, Dongping TU. Bioinformatics and Tissue-specific Expression Analysis of YUCCA Gene Family in Huperzia serrata[J]. Journal of Agricultural Science and Technology, 2025, 27(10): 72-83.

图/表 12

参考文献 38

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网站平台 Website platform	网址 Website	功能 Function
BLAST	https：//blast.ncbi.nlm.nih.gov/Blast.cgi	序列比对筛选基因 Screening genes by sequence alignment
ORF Finder	https：//www.ncbi.nlm.nih.gov/orffinder	获得潜在的蛋白质编码片段 Obtain potential protein-coding fragments
SMART	http：//smart.embl-heidelberg.de/	结构域预测 Domain prediction
InterPro	https：//www.ebi.ac.uk/interpro/search/sequence/	结构域预测 Domain prediction
Batch CD-Search	https：//www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi	结构域预测 Domain prediction
ExPAsy	https：//web.expasy.org/protparam/	理化性质分析 Analysis of physicochemical property
Plant-mPLoc	http：//www.csbio.sjtu.edu.cn/bioinf/plant-multi/	亚细胞定位预测 Subcellular localization prediction
DeepTMHMM	https：//dtu.biolib.com/DeepTMHMM	跨膜预测 Transmembrane prediction
SignalP-6.0	https：//services.healthtech.dtu.dk/services/SignalP-6.0/	信号肽预测 Signal peptide prediction
Prabi	https：//npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl？page=npsa_sopma.html	二级结构预测 Secondary structure prediction
Phyre2	http：//www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi？id=index	三级结构预测 Tertiary structure prediction
MEME Suite 5.5.5	https：//meme-suite.org/meme/tools/meme	保守基序预测 Conserved motif prediction
Plantcare	https：//bioinformatics.psb.ugent.be/webtools/plantcare/html/	顺式作用元件预测 Cis-acting element prediction

网站平台 Website platform	网址 Website	功能 Function
BLAST	https：//blast.ncbi.nlm.nih.gov/Blast.cgi	序列比对筛选基因 Screening genes by sequence alignment
ORF Finder	https：//www.ncbi.nlm.nih.gov/orffinder	获得潜在的蛋白质编码片段 Obtain potential protein-coding fragments
SMART	http：//smart.embl-heidelberg.de/	结构域预测 Domain prediction
InterPro	https：//www.ebi.ac.uk/interpro/search/sequence/	结构域预测 Domain prediction
Batch CD-Search	https：//www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi	结构域预测 Domain prediction
ExPAsy	https：//web.expasy.org/protparam/	理化性质分析 Analysis of physicochemical property
Plant-mPLoc	http：//www.csbio.sjtu.edu.cn/bioinf/plant-multi/	亚细胞定位预测 Subcellular localization prediction
DeepTMHMM	https：//dtu.biolib.com/DeepTMHMM	跨膜预测 Transmembrane prediction
SignalP-6.0	https：//services.healthtech.dtu.dk/services/SignalP-6.0/	信号肽预测 Signal peptide prediction
Prabi	https：//npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl？page=npsa_sopma.html	二级结构预测 Secondary structure prediction
Phyre2	http：//www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi？id=index	三级结构预测 Tertiary structure prediction
MEME Suite 5.5.5	https：//meme-suite.org/meme/tools/meme	保守基序预测 Conserved motif prediction
Plantcare	https：//bioinformatics.psb.ugent.be/webtools/plantcare/html/	顺式作用元件预测 Cis-acting element prediction

蛋白 Protein	氨基酸数量Number of amino acids/aa	分子量 Molecular weight/Da	等电点 pI	不稳定指数Instability index	脂溶指数Aliphatic index	平均亲水性指数 GRAVY
HsYUCCA1	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA2	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA3	167	17 161.46	5.30	41.09	86.59	0.166
HsYUCCA4	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA5	410	44 864.99	8.54	45.29	77.12	-0.260
HsYUCCA6	410	44 864.99	8.54	45.29	77.12	-0.260
HsYUCCA7	150	16 105.53	8.83	54.93	85.93	-0.198
HsYUCCA8	247	27 058.52	4.58	40.04	92.83	-0.039
HsYUCCA9	244	28 655.83	7.56	28.72	88.65	-0.505
HsYUCCA10	212	24 521.68	5.60	42.25	63.02	-0.804
HsYUCCA11	407	46 074.16	9.46	27.67	77.57	-0.354
HsYUCCA12	197	22 763.87	9.63	23.84	105.33	0.226
HsYUCCA13	150	16 105.53	8.83	54.93	85.93	-0.198
HsYUCCA14	354	28 602.97	4.62	42.33	97.57	-0.019
HsYUCCA15	161	17 571.91	4.36	48.24	85.59	-0.081
HsYUCCA16	330	37 721.64	9.01	44.11	80.12	-0.488
HsYUCCA17	544	59 058.24	4.82	40.04	98.47	0.011
HsYUCCA18	150	17 856.82	9.22	38.15	104.73	-0.191

蛋白 Protein	氨基酸数量Number of amino acids/aa	分子量 Molecular weight/Da	等电点 pI	不稳定指数Instability index	脂溶指数Aliphatic index	平均亲水性指数 GRAVY
HsYUCCA1	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA2	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA3	167	17 161.46	5.30	41.09	86.59	0.166
HsYUCCA4	207	22 567.66	5.97	45.77	83.04	-0.338
HsYUCCA5	410	44 864.99	8.54	45.29	77.12	-0.260
HsYUCCA6	410	44 864.99	8.54	45.29	77.12	-0.260
HsYUCCA7	150	16 105.53	8.83	54.93	85.93	-0.198
HsYUCCA8	247	27 058.52	4.58	40.04	92.83	-0.039
HsYUCCA9	244	28 655.83	7.56	28.72	88.65	-0.505
HsYUCCA10	212	24 521.68	5.60	42.25	63.02	-0.804
HsYUCCA11	407	46 074.16	9.46	27.67	77.57	-0.354
HsYUCCA12	197	22 763.87	9.63	23.84	105.33	0.226
HsYUCCA13	150	16 105.53	8.83	54.93	85.93	-0.198
HsYUCCA14	354	28 602.97	4.62	42.33	97.57	-0.019
HsYUCCA15	161	17 571.91	4.36	48.24	85.59	-0.081
HsYUCCA16	330	37 721.64	9.01	44.11	80.12	-0.488
HsYUCCA17	544	59 058.24	4.82	40.04	98.47	0.011
HsYUCCA18	150	17 856.82	9.22	38.15	104.73	-0.191

蛋白 Protein	亚细胞定位 Subcellular localization	信号肽 Signal peptide	跨膜Transmembrane
HsYUCCA1	线粒体 Mitochondrion	无No	1
HsYUCCA2	线粒体 Mitochondrion	无No	1
HsYUCCA3	叶绿体 Chloroplast	无No	1
HsYUCCA4	线粒体 Mitochondrion	无No	1
HsYUCCA5	叶绿体，细胞质 Chloroplast， cytoplasm	无No	0
HsYUCCA6	叶绿体，细胞质 Chloroplast， cytoplasm	无No	0
HsYUCCA7	线粒体 Mitochondrion	无No	1
HsYUCCA8	细胞核 Nucleus	无No	0
HsYUCCA9	细胞核 Nucleus	无No	0
HsYUCCA10	细胞质，过氧化物酶体 Cytoplasm， peroxisome	无No	0
HsYUCCA11	叶绿体，细胞质 Chloroplast， cytoplasm	无No	0
HsYUCCA12	细胞膜 Cell membrane	无No	2
HsYUCCA13	线粒体 Mitochondrion	无No	1
HsYUCCA14	叶绿体，细胞核 Chloroplast， nucleus	无No	0
HsYUCCA15	细胞核 Nucleus	无No	0
HsYUCCA16	叶绿体 Chloroplast	无No	0
HsYUCCA17	细胞核 Nucleus	无No	0
HsYUCCA18	细胞核 Nucleus	无No	0