蕙兰一个PEBP家族基因的克隆及生物信息学分析

doi:10.3969/j.issn.1004-1524.2022.08.12

浙江农业学报 ›› 2022, Vol. 34 ›› Issue (8): 1679-1691.DOI: 10.3969/j.issn.1004-1524.2022.08.12

蕙兰一个PEBP家族基因的克隆及生物信息学分析

楚志刚¹(), 田云芳²^,³^,^*()

1.郑州师范学院信息科学与技术学院,河南郑州 450044
2.郑州师范学院生命科学学院,河南郑州 450044
3.郑州市观赏药用特色资源植物重点实验室,河南郑州 450044

收稿日期:2021-01-25 出版日期:2022-08-25 发布日期:2022-08-26
作者简介:*田云芳,E-mail: tianyunfang2011@163.com
楚志刚(1980—),男,河南荥阳人,硕士,讲师,研究方向为生物信息学。E-mail: chu_zhigang@163.com
通讯作者: 田云芳
基金资助:
河南省科技攻关计划(212102110184);河南省高等学校重点科研项目(22A210026);河南省高等学校青年骨干教师培养计划(2018GGJS162)

Cloning and bioinformatics analysis of a PEBP family gene from Cymbidium faberi

CHU Zhigang¹(), TIAN Yunfang²^,³^,^*()

1. College of Information Science and Technology, Zhengzhou Normal University, Zhengzhou 450044, China
2. College of Life Sciences, Zhengzhou Normal University, Zhengzhou 450044, China
3. Zhengzhou Key Laboratory of Ornamental and Medicinal Resources Plants, Zhengzhou 450044, China

Received:2021-01-25 Online:2022-08-25 Published:2022-08-26
Contact: TIAN Yunfang

摘要/Abstract

摘要：

为了初步探究蕙兰磷脂酰乙醇胺结合蛋白(phosphatidyl ethanolamine-binding proteins, PEBP)基因的特征与功能,以蕙兰花蕾期叶片为材料,利用反转录PCR(RT-PCR)结合cDNA末端快速扩增(RACE)技术克隆基因,使用在线生物信息学工具进行蛋白结构与功能预测,通过R语言和3个在线软件(CodonW、CHIPS和CUSP)分析该基因的密码子偏好性。结果表明,克隆得到的蕙兰PEBP基因包含531 bp长度的开放阅读框(ORF),对应编码氨基酸176个。该基因命名为CfPEBP(登录号MT795710)。生物信息学分析表明,CfPEBP分子式为C₈₈₂H₁₃₆₆N₂₅₄O₂₆₀S₅,分子量为19 848.39 u;等电点为 6.42;具有15个磷酸化位点。CfPEBP蛋白无信号肽结构域,具有PEBP功能域。进化树分析结果表明,CfPEBP蛋白与春兰FT进化距离最近,同源性为100%。分析显示,CfPEBP的密码子偏好性表现较弱;依据同义密码子相对使用度(RSCU)分析较强偏性密码子有GGC、AGA、AGU、AAG、CCA、CUC(RSCU≥2.00)。18个物种PEBP基因RSCU值分析表明,蕙兰HQ164434、文心兰KJ909968、文心兰EU583502、石斛MF063061、香蕉KF853468、牵牛AB154823的密码偏好性较强,均有25个以上RSCU值>1. 00的密码子。PEBP家族基因对于GGC、AGG、AGA、AGC、AGU、UGC、GAG、AAG、UAC、GCC、CCA、CUC的偏好性超过其他密码子。CfPEBP基因在蕙兰盛花期叶中相对表达量最高,花蕾期花蕾和盛花期花葶中表达量次之,其他组织几乎不表达。本研究为蕙兰PEBP家族基因功能的进一步研究提供了基础。

关键词: 蕙兰, PEBP, 生物信息学分析, 密码子偏好性, 表达

Abstract:

In order to explore the characteristics and function of PEBP gene family in Cymbidium faberi, the gene was cloned by reverse transcription-polymerase chain reaction (RT-PCR) combined with rapid-amplification of cDNA ends (RACE). R language, CodonW, CHIPS and CUSP software were used to analyze the codon preference, and the protein structure and function of the gene were predicted by using bioinformatics tools. The results showed that the cDNA sequence of PEBP gene contained 531 bp open reading frame (ORF) and encoded 176 amino acids. The gene was named as CfPEBP(Accession No. MT795710). The molecular formula of CfPEBP was C₈₈₂H₁₃₆₆N₂₅₄O₂₆₀S₅ with molecular weight of 19 848.39 u, pI of 6.42, and phosphorylation sites of 15. CfPEBP protein has no signal peptide domain and has PEBP functional domain. Phylogenetic tree analysis showed that CfPEBP protein had the closest evolutionary distance with FT gene of Cymbidium goeringii, and the homology was 100%. Codon preference analysis showed that the codon preference of CfPEBP was not obvious; based on the relative synonymous codon usage (RSCU) value, GGC, AGA, AGU, AAG, CCA, CUC (RSCU≥2) were the most preferred codons. The RSCU value analysis of PEBP gene in 18 species showed that there were more than 25 codons with RSCU value>1 in Cymbidium faberi, Oncidium hybrid(KJ909968), Oncidium hybrid(EU583502), Dendrobium hybrid(MF063061), Musa acuminata(KF853468) and Ipomoea nil(AB154823). PEBP family genes had more preference than other codons for GGC, AGG, AGA, AGC, AGU, UGC, GAG, AAG, UAC, GCC, CCA, CUC. The relative expression level of CfPEBP gene was the highest in the leaves of Cymbidium faberi at flowering stage, followed by flower bud at bud stage and inflorescence rachis at full-blossom stage. This study provided the basis for further study on the function of CfPEBP gene.

Key words: Cymbidium faberi, PEBP, bioinformatics analysis, codon usage bias, expression

中图分类号:

S682.31

楚志刚, 田云芳. 蕙兰一个PEBP家族基因的克隆及生物信息学分析[J]. 浙江农业学报, 2022, 34(8): 1679-1691.

CHU Zhigang, TIAN Yunfang. Cloning and bioinformatics analysis of a PEBP family gene from Cymbidium faberi[J]. Acta Agriculturae Zhejiangensis, 2022, 34(8): 1679-1691.

图/表 12

参考文献 44

[1]	孙崇波, 刘玫, 施季森, 等. 蕙兰种子无菌萌发及植株再生[J]. 浙江农业学报, 2008, 20(4): 231-235.
	SUN C B, LIU M, SHI J S, et al. Aseptic germination of Cymbidium faberi seeds and in vitro plant regeneration[J]. Acta Agriculturae Zhejiangensis, 2008, 20(4): 231-235. (in Chinese with English abstract)
[2]	陆顺教, 易双双, 廖易, 等. 兰花花期调控技术及相关分子生物学研究进展[J]. 江苏农业科学, 2017, 45(18): 25-30.
	LU S J, YI S S, LIAO Y, et al. Research progress on flowering regulation technology and related molecular biology of orchid[J]. Jiangsu Agricultural Sciences, 2017, 45(18): 25-30. (in Chinese)
[3]	BRADLEY D, CARPENTER R, COPSEY L, et al. Control of inflorescence architecture in Antirrhinum[J]. Nature, 1996, 379(6568): 791-797. DOI URL
[4]	KARDAILSKY I, SHUKLA V K, AHN J H, et al. Activation tagging of the floral inducer FT[J]. Science, 1999, 286(5446): 1962-1965. DOI URL
[5]	KOBAYASHI Y, KAYA H, GOTO K, et al. A pair of related genes with antagonistic roles in mediating flowering signals[J]. Science, 1999, 286(5446): 1960-1962. DOI URL
[6]	CHARDON F, DAMERVAL C. Phylogenomic analysis of the PEBP gene family in cereals[J]. Journal of Molecular Evolution, 2005, 61(5): 579-590. DOI URL
[7]	袁玺垒, 王振山, 贾小平, 等. 光周期调控植物开花分子机制以及CCT基因家族研究进展[J]. 浙江农业学报, 2020, 32(6): 1133-1140. DOI
	YUAN X L, WANG Z S, JIA X P, et al. Research advances on molecular mechanisms of photoperiod-regulation plant flowering and CCT gene family[J]. Acta Agriculturae Zhejiangensis, 2020, 32(6): 1133-1140. (in Chinese with English abstract)
[8]	YAMAGUCHI A, KOBAYASHI Y, GOTO K, et al. TWIN SISTER OF FT(TSF) acts as a floral pathway integrator redundantly with FT[J]. Plant and Cell Physiology, 2005, 46(8): 1175-1189. DOI URL
[9]	BRADLEY D, RATCLIFFE O, VINCENT C, et al. Inflorescence commitment and architecture in Arabidopsis[J]. Science, 1997, 275(5296): 80-83. DOI URL
[10]	XI W Y, LIU C, HOU X L, et al. Mother of FT and TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis[J]. The Plant Cell, 2010, 22(6): 1733-1748. DOI URL
[11]	NAKAMURA S, ABE F, KAWAHIGASHI H, et al. A wheat homolog of mother of FT and TFL1 acts in the regulation of germination[J]. The Plant Cell, 2011, 23(9): 3215-3229. DOI URL
[12]	HELLER W P, YING Z T, DAVENPORT T L, et al. Identification of members of the Dimocarpus longan flowering locus T gene family with divergent functions in flowering[J]. Tropical Plant Biology, 2014, 7(1): 19-29. DOI URL
[13]	DING F, ZHANG S W, CHEN H B, et al. Promoter difference of LcFT1 is a leading cause of natural variation of flowering timing in different Litchi cultivars (Litchi chinensis Sonn.)[J]. Plant Science, 2015, 241: 128-137. DOI URL
[14]	ZHOU S S, JIANG L, GUAN S X, et al. Expression profiles of five FT-like genes and functional analysis of PhFT-1 in a Phalaenopsis hybrid[J]. Electronic Journal of Biotechnology, 2018, 31: 75-83. DOI URL
[15]	HIGUCHI Y, NARUMI T, ODA A, et al. The gated induction system of a systemic floral inhibitor, antiflorigen, determines obligate short-day flowering in chrysanthemums[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(42): 17137-17142.
[16]	OTAGAKI S, OGAWA Y, HIBRAND-SAINT OYANT L, et al. Genotype of FLOWERING LOCUS T homologue contributes to flowering time differences in wild and cultivated roses[J]. Plant Biology (Stuttgart, Germany), 2015, 17(4): 808-815. DOI URL
[17]	WU L, LI F, DENG Q H, et al. Identification and characterization of the FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family in Petunia[J]. DNA and Cell Biology, 2019, 38(9): 982-995. DOI URL
[18]	BLACKMAN B K, STRASBURG J L, RADUSKI A R, et al. The role of recently derived FT paralogs in sunflower domestication[J]. Current Biology, 2010, 20(7): 629-635. DOI URL
[19]	LEEGGANGERS H A, ROSILIO-BRAMI T, BIGAS-NADAL J, et al. Tulipa gesneriana and Lilium longiflorum PEBP genes and their putative roles in flowering time control[J]. Plant and Cell Physiology, 2017, 59(1): 90-106. DOI URL
[20]	XIANG L, LI X B, QIN D H, et al. Functional analysis of FLOWERING LOCUS T orthologs from spring orchid (Cymbidium goeringii Rchb. f.) that regulates the vegetative to reproductive transition[J]. Plant Physiology and Biochemistry, 2012, 58: 98-105. DOI URL
[21]	PANJAMA K, SUZUKI E, OTANI M, et al. Isolation and functional analysis of FLOWERING LOCUS T orthologous gene from Vanda hybrid[J]. Journal of Plant Biochemistry and Biotechnology, 2019, 28(4): 374-381. DOI URL
[22]	CHEN M, PENFIELD S. Feedback regulation of COOLAIR expression controls seed dormancy and flowering time[J]. Science, 2018, 360(6392): 1014-1017. DOI URL
[23]	FREIMAN A, GOLOBOVITCH S, YABLOVITZ Z, et al. Expression of flowering locus T2 transgene from Pyrus communis L. delays dormancy and leaf senescence in Malus×domestica Borkh, and causes early flowering in tobacco[J]. Plant Science, 2015, 241: 164-176. DOI URL
[24]	GAO X, WALWORTH A E, MACKIE C, et al. Overexpression of blueberry FLOWERING LOCUS T is associated with changes in the expression of phytohormone-related genes in blueberry plants[J]. Horticulture Research, 2016, 3(10.1038): hortres.2016.53.
[25]	SRINIVASAN C, DARDICK C, CALLAHAN A, et al. Plum (Prunus domestica) trees transformed with poplar FT1 result in altered architecture, dormancy requirement, and continuous flowering[J]. PLoS One, 2012, 7(7): e40715.
[26]	LEE R, BALDWIN S, KENEL F, et al. FLOWERING LOCUS T genes control onion bulb formation and flowering[J]. Nature Communications, 2013, 4: 2884. DOI URL
[27]	KINOSHITA T, ONO N, HAYASHI Y, et al. FLOWERING LOCUS T regulates stomatal opening[J]. Current Biology, 2011, 21(14): 1232-1238. DOI URL
[28]	田云芳, 袁秀云, 蒋素华, 等. 蕙兰CfMADS1基因的克隆及其时空表达特性[J]. 西北农林科技大学学报(自然科学版), 2015, 43(7): 143-149.
	TIAN Y F, YUAN X Y, JIANG S H, et al. Cloning and spatiotemporal expression of CfMADS1 gene in orchid(Cymbidium faberi)[J]. Journal of Northwest A & F University (Natural Science Edition), 2015, 43(7): 143-149. (in Chinese with English abstract)
[29]	CZECHOWSKI T, STITT M, ALTMANN T, et al. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis[J]. Plant Physiology, 2005, 139(1): 5-17. DOI URL
[30]	冯琛, 汤浩茹, 江雷雨, 等. 红蓝光对草莓转录组特异表达基因密码子使用偏好性的影响[J]. 浙江农业学报, 2017, 29(4): 566-574. DOI
	FENG C, TANG H R, JIANG L Y, et al. Analysis of codon usage bias of specific genes in strawberry transcriptome under the red and blue light[J]. Acta Agriculturae Zhejiangensis, 2017, 29(4): 566-574. (in Chinese with English abstract) DOI
[31]	CORBIT K C, TRAKUL N, EVES E M, et al. Activation of Raf-1 signaling by protein kinase C through a mechanism involving raf kinase inhibitory protein[J]. Journal of Biological Chemistry, 2003, 278(15): 13061-13068. DOI URL
[32]	于秀立. 陆地棉MFT-like亚家族基因的克隆与功能研究[D]. 石河子: 石河子大学, 2019.
	YU X L. Cloning and functional study of MFT-like genes in Gossypium hirsutum L[D]. Shihezi: Shihezi University, 2019. (in Chinese with English abstract)
[33]	刘薇. 大豆开花调控基因GmFT1a的克隆和功能研究[D]. 北京: 中国农业科学院, 2018.
	LIU W. Cloning and functional analysis of GmFT1a, a flowering regulating ft homolog in soybean[D]. Beijing: Chinese Academy of Agricultural Sciences, 2018. (in Chinese with English abstract)
[34]	李喜莲, 杨元杰, 李倩, 等. 螯虾次目功能基因密码子偏好性研究[J]. 浙江农业学报, 2014, 26(4): 862-867.
	LI X L, YANG Y J, LI Q, et al. Analysis on codon bias of functional gene of Astacidea[J]. Acta Agriculturae Zhejiangensis, 2014, 26(4): 862-867. (in Chinese with English abstract)
[35]	宗秋芳, 黄焱杰, 吴丽思, 等. 猪Claudin家族基因密码子使用偏好性分析[J]. 浙江农业学报, 2018, 30(12): 2007-2017. DOI
	ZONG Q F, HUANG Y J, WU L S, et al. Analysis of genetic codon usage preference in pig Claudin family[J]. Acta Agriculturae Zhejiangensis, 2018, 30(12): 2007-2017. (in Chinese with English abstract)
[36]	晁岳恩, 吴政卿, 杨会民, 等. 11种植物psbA基因的密码子偏好性及聚类分析[J]. 核农学报, 2011, 25(5): 927-932.
	CHAO Y E, WU Z Q, YANG H M, et al. Cluster analysis and codon usage bias studies on psbA genes from 11 plant species[J]. Journal of Nuclear Agricultural Sciences, 2011, 25(5): 927-932. (in Chinese with English abstract)
[37]	郭秀丽, 王玉, 杨路成, 等. 茶树CBF1基因密码子使用特性分析[J]. 遗传, 2012, 34(12): 1614-1623.
	GUO X L, WANG Y, YANG L C, et al. Analysis of codon use features of CBF1 gene in Camellia sinensis[J]. Hereditas, 2012, 34(12): 1614-1623. (in Chinese with English abstract)
[38]	孙晶, 何涛, 万闰兰, 等. 铁皮石斛尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)的密码子偏好性分析[J]. 应用与环境生物学报, 2014, 20(5): 759-766.
	SUN J, HE T, WAN R L, et al. The codon usage bias of UDP-glucose pyrophosphorylase gene (UGP) in Dendrobium officinale[J]. Chinese Journal of Applied and Environmental Biology, 2014, 20(5): 759-766. (in Chinese with English abstract)
[39]	聂江婷, 白云凤, 贺飞燕, 等. 籽粒苋丙酮酸磷酸二激酶(PPDK)基因的密码子偏好性[J]. 植物学报, 2014, 49(6): 672-681. DOI
	NIE J T, BAI Y F, HE F Y, et al. Codon bias of pyruvate orthophosphate dikinase gene in Amaranthus hypochondriacus[J]. Chinese Bulletin of Botany, 2014, 49(6): 672-681. (in Chinese with English abstract) DOI URL
[40]	赖瑞联, 林玉玲, 钟春水, 等. 龙眼生长素受体基因TIR1密码子偏好性分析[J]. 园艺学报, 2016, 43(4): 771-780.
	LAI R L, LIN Y L, ZHONG C S, et al. Analysis of codon bias of auxin receptor gene TIR1 in Dimocarpus longan[J]. Acta Horticulturae Sinica, 2016, 43(4): 771-780. (in Chinese with English abstract)
[41]	柏锡, 徐建震, 李琳, 等. 马铃薯密码子用法分析及其在t-PA基因密码子改造上的应用[J]. 遗传, 2004, 26(1): 75-83.
	BAI X, XU J Z, LI L, et al. Analysis of codon usage in potato and its application in the modification of t-PA gene[J]. Hereditas(Beijing), 2004, 26(1): 75-83. (in Chinese with English abstract)
[42]	杨江科, 严翔翔, 张正平, 等. 二步法黑曲霉脂肪酶基因lipA的全基因合成及其在毕赤酵母中的高效表达[J]. 生物工程学报, 2009, 25(3): 381-387.
	YANG J K, YAN X X, ZHANG Z P, et al. Two-step synthesis of the full length Aspergillus niger lipase gene lipA leads to high-level expression in Pichia pastoris[J]. Chinese Journal of Biotechnology, 2009, 25(3): 381-387. (in Chinese with English abstract)
[43]	杜致辉, 杨澜, 姚新转, 等. 黑喉石斛DoFT1基因在花发育过程中的表达模式分析及功能验证[J]. 热带作物学报, 2021, 42(4): 951-957.
	DU Z H, YANG L, YAO X Z, et al. Expression pattern analysis of Dendrobium ochreatum DoFT1 gene during flower development and its functional verification[J]. Chinese Journal of Tropical Crops, 2021, 42(4): 951-957. (in Chinese with English abstract)
[44]	孙崇波, 向林, 李小白, 等. 蕙兰Flowering locus T基因的克隆及其对开花的影响[J]. 中国农业科学, 2013, 46(7): 1419-1425.
	SUN C B, XIANG L, LI X B, et al. Isolation of Flowering locus T ortholog and the effects on blooming of Cymbidium faberi[J]. Scientia Agricultura Sinica, 2013, 46(7): 1419-1425. (in Chinese with English abstract)

扩增方式 Amplification sort	引物序列 Primer sequences( 5'-3')
Specific amplification	PEBP-F: CCTTCAGCAGTAGTGGAGCAG PEBP-R: GGCGAAGTCACGGGTGTT
3'-RACE	3F1: TCAACACCCGTGACTTCG 3F2: TTTGGCAGCGAAATAGTGT
5'-RACE	5R1: ATCGGTGACCAACCAGTGTAAG 5R2: TGAAAGAGCACGAAGACG
RT-qPCR-PEBP	PEBP-QF: CATACACCGCTTCGTCTT PEBP-QR: ATCCTGCATCCTTCTTCC
RT-qPCR-ACT	ACT-QF: GCCATCCATGATTGGTAT ACT-QR: ATCTGCTGAAAGGTGCTG
RT-qPCR-UBQ3	UBQ3-QF: GGATGGGCGTACTTTAGCA UBQ3-QR: GTTCGGGCACTCCTTTCTG

扩增方式 Amplification sort	引物序列 Primer sequences( 5'-3')
Specific amplification	PEBP-F: CCTTCAGCAGTAGTGGAGCAG PEBP-R: GGCGAAGTCACGGGTGTT
3'-RACE	3F1: TCAACACCCGTGACTTCG 3F2: TTTGGCAGCGAAATAGTGT
5'-RACE	5R1: ATCGGTGACCAACCAGTGTAAG 5R2: TGAAAGAGCACGAAGACG
RT-qPCR-PEBP	PEBP-QF: CATACACCGCTTCGTCTT PEBP-QR: ATCCTGCATCCTTCTTCC
RT-qPCR-ACT	ACT-QF: GCCATCCATGATTGGTAT ACT-QR: ATCTGCTGAAAGGTGCTG
RT-qPCR-UBQ3	UBQ3-QF: GGATGGGCGTACTTTAGCA UBQ3-QR: GTTCGGGCACTCCTTTCTG

密码子 Codon	氨基酸 AA	比例 Fraction	频率 Frequency	数目 Number	密码子 Codon	氨基酸 AA	比例 Fraction	频率 Frequency	数目 Number
GCA	A	0.246	13.354	43	CCA	P	0.407	29.193	94
GCC	A	0.457	24.845	80	CCC	P	0.173	12.422	40
GCG	A	0.131	7.143	23	CCG	P	0.26	18.634	60
GCT	A	0.166	9.006	29	CCT	P	0.16	11.491	37
TGC	C	0.844	11.801	38	CAA	Q	0.242	9.006	29
TGT	C	0.156	2.174	7	CAG	Q	0.758	28.261	91
GAC	D	0.360	21.118	68	AGA	R	0.360	34.783	112
GAT	D	0.640	37.578	121	AGG	R	0.267	25.776	83
GAA	E	0.200	9.317	30	CGA	R	0.042	4.037	13
GAG	E	0.800	37.267	120	CGC	R	0.113	10.87	5
TTC	F	0.719	35.714	115	CGG	R	0.122	11.801	38
TTT	F	0.281	13.975	45	CGT	R	0.096	9.317	30
GGA	G	0.217	18.012	58	AGC	S	0.263	16.149	52
GGC	G	0.517	42.857	138	AGT	S	0.283	17.391	56
GGG	G	0.135	11.180	36	TCA	S	0.116	7.143	3
GGT	G	0.131	10.870	35	TCC	S	0.116	7.143	23
CAC	H	0.656	13.043	42	TCG	S	0.096	5.901	19
CAT	H	0.344	6.832	22	TCT	S	0.126	7.764	25
ATA	I	0.333	9.938	32	ACA	T	0.267	16.77	54
ATC	I	0.344	10.248	33	ACC	T	0.282	17.702	57
ATT	I	0.323	9.627	31	ACG	T	0.163	10.248	3
AAA	K	0.130	0.932	3	ACT	T	0.287	18.012	58
AAG	K	0.870	6.211	20	GTA	V	0.128	13.975	45
CTA	L	0.093	7.453	24	GTC	V	0.322	35.093	113
CTC	L	0.323	25.776	83	GTG	V	0.319	34.783	112
CTG	L	0.144	11.491	37	GTT	V	0.231	25.155	1
CTT	L	0.210	16.77	54	TGG	W	1.000	11.18	36
TTA	L	0.105	8.385	27	TAC	Y	0.729	29.193	94
TTG	L	0.125	9.938	32	TAT	Y	0.271	10.87	35
ATG	M	1.000	20.807	67	TAA	*	0.056	0.311	1
AAC	N	0.473	19.255	62	TAG	*	0.222	1.242	4
AAT	N	0.527	21.429	69	TGA	*	0.722	4.037	13

密码子 Codon	氨基酸 AA	比例 Fraction	频率 Frequency	数目 Number	密码子 Codon	氨基酸 AA	比例 Fraction	频率 Frequency	数目 Number
GCA	A	0.246	13.354	43	CCA	P	0.407	29.193	94
GCC	A	0.457	24.845	80	CCC	P	0.173	12.422	40
GCG	A	0.131	7.143	23	CCG	P	0.26	18.634	60
GCT	A	0.166	9.006	29	CCT	P	0.16	11.491	37
TGC	C	0.844	11.801	38	CAA	Q	0.242	9.006	29
TGT	C	0.156	2.174	7	CAG	Q	0.758	28.261	91
GAC	D	0.360	21.118	68	AGA	R	0.360	34.783	112
GAT	D	0.640	37.578	121	AGG	R	0.267	25.776	83
GAA	E	0.200	9.317	30	CGA	R	0.042	4.037	13
GAG	E	0.800	37.267	120	CGC	R	0.113	10.87	5
TTC	F	0.719	35.714	115	CGG	R	0.122	11.801	38
TTT	F	0.281	13.975	45	CGT	R	0.096	9.317	30
GGA	G	0.217	18.012	58	AGC	S	0.263	16.149	52
GGC	G	0.517	42.857	138	AGT	S	0.283	17.391	56
GGG	G	0.135	11.180	36	TCA	S	0.116	7.143	3
GGT	G	0.131	10.870	35	TCC	S	0.116	7.143	23
CAC	H	0.656	13.043	42	TCG	S	0.096	5.901	19
CAT	H	0.344	6.832	22	TCT	S	0.126	7.764	25
ATA	I	0.333	9.938	32	ACA	T	0.267	16.77	54
ATC	I	0.344	10.248	33	ACC	T	0.282	17.702	57
ATT	I	0.323	9.627	31	ACG	T	0.163	10.248	3
AAA	K	0.130	0.932	3	ACT	T	0.287	18.012	58
AAG	K	0.870	6.211	20	GTA	V	0.128	13.975	45
CTA	L	0.093	7.453	24	GTC	V	0.322	35.093	113
CTC	L	0.323	25.776	83	GTG	V	0.319	34.783	112
CTG	L	0.144	11.491	37	GTT	V	0.231	25.155	1
CTT	L	0.210	16.77	54	TGG	W	1.000	11.18	36
TTA	L	0.105	8.385	27	TAC	Y	0.729	29.193	94
TTG	L	0.125	9.938	32	TAT	Y	0.271	10.87	35
ATG	M	1.000	20.807	67	TAA	*	0.056	0.311	1
AAC	N	0.473	19.255	62	TAG	*	0.222	1.242	4
AAT	N	0.527	21.429	69	TGA	*	0.722	4.037	13

物种(核酸登录号)	U3s	C3s	A3s	G3s	CAI	FOP	ENC	GC3s	GC	RSCU>1	RSCU>1.5
蕙兰Cymbidium faberi PEBP (MT795710)	0.2968	0.3548	0.3053	0.2381	0.161	0.363	57.37	0.497	0.513	22	10
建兰Cymbidium ensifolium FT(HM803115)	0.2968	0.3548	0.2901	0.2540	0.163	0.368	55.83	0.509	0.517	23	10
水稻Oryza sativa RFT1(AB809564)	0.1753	0.5065	0.1069	0.4048	0.223	0.476	41.22	0.759	0.605	24	17
山白竹Sasa veitchii SvFT1(LC020117)	0.1569	0.4837	0.1250	0.4355	0.195	0.476	47.59	0.762	0.610	24	16
蝴蝶兰Phalaenopsis aphrodite FT1(KJ609179)	0.3419	0.2903	0.3939	0.1760	0.138	0.308	48.53	0.390	0.468	22	12
春兰Cymbidium goeringii FT(HM106985)	0.2968	0.3548	0.3053	0.2381	0.161	0.363	57.37	0.497	0.513	22	10
春兰Cymbidium goeringii FT(HM120863)	0.2968	0.3548	0.2977	0.2460	0.161	0.363	57.14	0.503	0.515	23	10
蕙兰Cymbidium faberi FT(HQ164434)	0.2839	0.3613	0.3130	0.2381	0.161	0.363	55.37	0.503	0.517	25	12
文心兰Oncidium hybrid OnFT(KJ909968)	0.3247	0.3052	0.3106	0.2619	0.181	0.404	51.93	0.468	0.492	25	12
墨兰Cymbidium sinense FT (HM120862)	0.2968	0.3548	0.2977	0.2460	0.163	0.368	56.06	0.503	0.515	22	10
文心兰Oncidium hybrid FT(EU583502)	0.3247	0.2857	0.3182	0.2778	0.172	0.392	54.53	0.462	0.491	28	11
石斛Dendrobium hybrid FT (MF063061)	0.3807	0.2841	0.2819	0.2695	0.158	0.350	52.47	0.447	0.481	27	13
香蕉Musa acuminata FT6 (KF853468)	0.2133	0.4200	0.2214	0.3651	0.162	0.400	50.17	0.641	0.560	25	14
野生稻Oryza rufipogon RFT1(KR423010)	0.1765	0.5098	0.1061	0.4016	0.228	0.476	41.23	0.759	0.607	24	16
蝴蝶兰Phalaenopsis hybrid FT (JX162558)	0.3312	0.2922	0.4015	0.1760	0.139	0.316	49.10	0.392	0.473	22	12
毛竹Phyllostachys edulis FTL1(KX714711)	0.0943	0.5094	0.0741	0.5038	0.217	0.517	38.22	0.855	0.670	21	19
绿竹Bambusa oldhamii FTL1 (KX714693)	0.0818	0.5220	0.0741	0.5038	0.217	0.523	37.60	0.866	0.674	21	19
牵牛Ipomoea nil PnFTA (AB154823)	0.3355	0.3484	0.2143	0.2975	0.241	0.497	55.12	0.533	0.538	26	11

蕙兰一个PEBP家族基因的克隆及生物信息学分析

Cloning and bioinformatics analysis of a PEBP family gene from Cymbidium faberi

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 12

参考文献 44

相关文章 15

编辑推荐

Metrics

本文评价

[1]	张均, 张博, 胡碧博, 刘京亮, 张晓宇, 李春阳, 熊盛婷, 郭彬彬, 王秀存, 马超. 小麦SWEET和SUT家族基因鉴定与表达分析[J]. 浙江农业学报, 2025, 37(9): 1825-1839.
[2]	蒋明, 张胜, 陈孝赏, 张慧娟. 西兰花灰霉病响应基因BoWRKY15的克隆与功能鉴定[J]. 浙江农业学报, 2025, 37(8): 1723-1732.
[3]	任晋东, 陈红林, 牛宝龙, 许晓军, 楼宝. 基于转录组分析挖掘罗氏沼虾新内参基因[J]. 浙江农业学报, 2025, 37(7): 1424-1429.
[4]	张悦宇, 黄美琦, 张琳, 齐颖, 李秋玲. bta-miR-146b对热应激奶牛乳腺上皮细胞乳蛋白合成信号通路的影响[J]. 浙江农业学报, 2025, 37(6): 1212-1220.
[5]	狄延翠, 嵇泽琳, 王媛媛, 娄世浩, 张涛, 国志信, 申顺善, 朴凤植, 杜南山, 董晓星, 董韩. 番茄SlMYB52基因鉴定、亚细胞定位及表达分析[J]. 浙江农业学报, 2025, 37(4): 808-819.
[6]	卢莉娜, 朱庆, 高美静, 谢雅晶, 刘贤金, 张志勇. 小菜蛾V-ATP酶A亚基表达丰度差异[J]. 浙江农业学报, 2025, 37(4): 839-846.
[7]	郑婷, 向江, 魏灵珠, 吴江, 程建徽. 基于WGCNA分析CPPU和TDZ对天工墨玉葡萄香气影响及关键基因挖掘[J]. 浙江农业学报, 2025, 37(2): 311-320.
[8]	张美莹, 莫倩, 齐秀双, 佟宁宁, 孔凡, 刘政安, 吕长平, 彭丽平. 牡丹PoLPAT2基因的克隆及表达分析[J]. 浙江农业学报, 2025, 37(2): 321-328.
[9]	金鑫, 林瑞, 刘岩, 许嘉盛, 陈琼琳, 袁璐, 薛大伟, 郑鹏, 徐盛春. 烟草ARF-GEF基因NtGNL2a启动子的克隆与表达分析[J]. 浙江农业学报, 2025, 37(10): 2032-2041.
[10]	廖小龙, 王兴胜, 陈勇, 李斌, 洪思丹, 梅利那, 国颖. 杨属植物HKT基因家族成员鉴定与盐胁迫下的表达模式分析[J]. 浙江农业学报, 2025, 37(10): 2104-2115.
[11]	玉妹, 毕冬琳, 郑天倚, 李琼毅. MAVS全长及其截短体真核表达载体的构建和鉴定[J]. 浙江农业学报, 2025, 37(1): 49-60.
[12]	欧晋稳, 张古文, 冯志娟, 王斌, 卜远鹏, 徐钰, 茹磊, 刘娜, 龚亚明. 大豆海藻糖-6-磷酸磷酸酶基因GmTPP的鉴定及其在生长发育和非生物胁迫响应中的表达分析[J]. 浙江农业学报, 2024, 36(9): 2031-2041.
[13]	孙培媛, 冉彬, 王佳蕊, 李洪有. 苦荞FtDELLA基因的克隆与表达分析[J]. 浙江农业学报, 2024, 36(8): 1709-1718.
[14]	朱贵爽, 李艳肖, 张安宁, 孙浩楠, 徐兴源, 李志刚, 向殿军. 蓖麻GeBP转录因子的全基因组鉴定与GeBP2基因的克隆、表达分析[J]. 浙江农业学报, 2024, 36(8): 1731-1740.
[15]	唐红, 关文志, 许晓军, 牛宝龙, 楼宝, 沈小明, 顾志敏. 三角鲂foxl2基因克隆和时空表达特征及EE2对其表达的影响[J]. 浙江农业学报, 2024, 36(8): 1789-1799.