Identification of Cytochrome P450 Family Genes in Melon and Expression Analysis in Response to Light Intensity

doi:10.16420/j.issn.0513-353x.2024-0990

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (12): 3271-3287.doi: 10.16420/j.issn.0513-353x.2024-0990

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Identification of Cytochrome P450 Family Genes in Melon and Expression Analysis in Response to Light Intensity

HAN Hongwei, CHANG Yanan, LIU Huifang, ZHUANG Hongmei, XING Jiayi, ZHANG Xiaoda, ZULIPIYE · Abudumilike, WANG Hao^*(), WANG Qiang^*

Xinjiang Vegetable Engineering Technology Research Center，Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables，Institute of Fruit and Vegetable Research，Xinjiang Uygur Autonomous Region Academy of Agricultural Sciences，Urumqi 830091，China

Received:2025-01-05 Revised:2025-09-03 Online:2025-12-25 Published:2025-12-20
Contact: WANG Hao, WANG Qiang

Abstract

Abstract:

To investigate the functions of cytochrome P450 monooxygenase（CYP450）gene family in Cucumis melo L.，the genomic data was analyzed using bioinformatics methods to identify the CYP450 family members in C. melo. The results revealed that a total of 195 full-length CYP450 genes were identified，belonging to 10 clan family clusters，and they were unevenly distributed on 12 chromosomes，contained 15 conserved motifs：The results of physical and chemical property analysis showed that the vast majority of CmCYP450 proteins were hydrophobic proteins，mainly localized in chloroplasts and plastid membranes：A large number of eukaryotic RNA polymerase Ⅱ binding sites，transcription factor binding sites，as well as photoresponsive and hormone responsive elements are present in the promoter regions of family genes. There were 69 CmCYP450 genes differentially expressed between yellow green leaf mutant Cmygl-1 and wild-type plants in response to different light intensities by RNA-seq. Among them，16 CmCYP450 genes are relatively highly expressed in melon leaves and show differential expression trends induced by different light radiation intensities，which may be involved in the regulation of leaf color variation of mutants.

Key words: Cucunis melo, CYP450 gene family, yellow-green leaf, mutant, light intensity, expression analysis

HAN Hongwei, CHANG Yanan, LIU Huifang, ZHUANG Hongmei, XING Jiayi, ZHANG Xiaoda, ZULIPIYE · Abudumilike, WANG Hao, WANG Qiang. Identification of Cytochrome P450 Family Genes in Melon and Expression Analysis in Response to Light Intensity[J]. Acta Horticulturae Sinica, 2025, 52(12): 3271-3287.

Figures/Tables 13

Table 1 Transmittance and light radiation intensity of different treatments

处理 Treatment	方法 Method	平均透光率/% Average transmittance	光辐射强度（× 10⁴lx） Light radiation intensity
强光（SW） Strong light	自然光（无遮光） Natural light（without shading）	100.0	6.08
亚强光（SN） Sub-strong light	距离植株生长点上方0.30 m覆盖一层棚膜 A layer of greenhouse film was covered 0.30 m above the plant growth point	78.2	4.75
遮荫（ZY） Shading	在SN处理的基础上再覆盖一层遮阳网 Based on the SN treatment，an additional layer of shading net was covered	28.7	1.74

Table 2 Pirmer sequences used for qRT-PCR analysis

引物名称Primer name	上游引物（5′-3′）Forward primer	下游引物（5′-3′）Reverse primer
MELO3C021434.2	GGTTCAGGCTTACAAGGCTAAT	CCACTCTCAAGGCATTCTACG
MELO3C009884.2	GGTGCCACTATTGTGTCTCTTC	GCCTATTCGGTTAGCAACTCTT
MELO3C002338.2	AAGCTCTTCCAATGCACCAAG	TGATGCCACAACACCAACAC
MELO3C018724.2	AGCATGGCAGGATTAGGAATTG	TTGTGGCGTTGGAGGAGTT
MELO3C011682.2	CATCTCGGCGTGGAAGGTAT	CGTGGCTGTCGTTCAAGTG
MELO3C011976.2	CGGCGGAGTATTGTCAGATG	CAACCAATCCAAGAACAACACA
MELO3C007154.2	TGAGCCACCATCCTACCTAAC	CACTTCCAACTCACGGTTCTT
MELO3C004214.2	GGAGAAGTGCCAGAGAACCT	TTTCACCCAGTTGCCCAATC
MELO3C022113.2	CGAGGCTGTCTGGTTCAAGA	CAATGACGGCGACGATGAG
MELO3C027057.2	GCAGACGCCAACGCCATTA	GCACGATCCAATTACGACGATT
MELO3C004135.2	CGGCAGCAACATTGAAACAA	TCTCACAAGCAGCAACAACA
MELO3C004201.2	ACACGACTTGGACTTGGAGAG	CCACAATGCTCAACAGAGACAA
MELO3C002187.2	CAATAGTCAGTGGCAACAACCT	GCGTAGCAGTTTCCGAATCAT
MELO3C006499.2	GGACAACGACTAATCGCCTAC	ATGATGGAATCGCTTGCTCTC
MELO3C026749.2	GGATGTGGTAGACTCTGTAGCA	CTTGACTGTCCTCCTGAGATTC
MELO3C026019.2	TTCCATTAACCAGTGCTGCTC	GCTCTTGACGAAGTGCTTGTA
MELO3C016167.2	TGTTGCCGTCCGATCCTTAT	CTTCCTCTTGCTCCTCTCCTT
MELO3C035538.2（CmCYP195）	TTGTCCAACTTGTTAGCGATGT	CTTGAATCCCGTGAAGATGGTA
MELO3C004801.2（CmCYP24）	GTCCAATCCTTCGCCTTCATT	GCCATTCGACAGATCACATCAT
MELO3C026260.2（CmCYP174）	TGCTTCCTCTTCTTCTTCTTCC	TTGGTGGAGATGGAGGTGAA
MELO3C011869.2（CmCYP79）	CACCGCTTCTCTGTCAACCT	TGAGCAATGGCAGCAAGATTC
MELO3C021842.2（CmCYP144）	ATCACTTCCAACCAACACAACA	CTGTAGGACCTGACACGAGAA
MELO3C015058.2（CmCYP101）	CCAGCACCACTGAGATATTGAG	TGAGAACATGAGAAGCAAGGAT
MELO3C013868.2（CmCYP95）	GCTTCGACGGCTGATAACAAT	GCAACTCCAATGGCTTCTCC

Fig. 1 Phylogenetic tree of CmCYP450s，AtCYP450s and OsCYP450s Red：CmCYP450s；Blue：AtCYP450s；Pink：OsCYP450s

Fig. 2 The Gene structure of CmCYP450 gene family members in Cucumis melo

Fig. 3 The conserved motifs of CmCYP450 gene family members in Cucumis melo

Fig. 4 Analysis of cis-acting elements of the CmCYP450 family promoter in Cucumis melo

Fig. 5 Chromosomal localization of CmCYP450 in Cucumis melo

Fig. 6 Gene replication and collinearity analysis of CmCYP450 The collinearity relationships of gene pairs are represented by colorful lines. Different chromosomes are represented by different colors

Fig. 7 Synteny analysis of P450 genes between the genomes of Cucumis melo，Arabidopsis thaliana and Oryza sativa The gray lines are all collinear relationships among different genomes，and the colored lines are collinear relationships among P450 gene family genes

Fig. 8 Protein interactions network diagram of P450 genes in Cucumis melo

Fig. 9 The heat map of differential expression of CmCYP450 under different light radiation intensities（A），Phenotypes of mutants and wild-type plants（B），Correlation analysis of relative expression levels between RNA seq and qRT PCR（C） The plant on the left in Figure B is the mutant Cmygl-1，and the plant on the right is the wild type

Fig. 10 Analysis of expression trends of some CmCYP450 genes using qRT-PCR（fold change）and RNA-seq（FPKM） SWWT：The wild type plants with strong light treatment；SNWT：The wild type plants with sub intense light treatment；ZYWT：The wild type plants with shade treatment；SNMT：The mutants with strong light treatment；SNMT：The mutants with sub intense light treatment；ZYMT：The mutants with shade treatment

Fig. 11 The expression trends of 16 CmCYP450 genes highly expressed in mutant leaves in response to different light radiation intensities FPKM：Fragments Per Kilobase of transcript per Million mapped reads. Different lowercase letter indicate significant differences at 0.05 level

References 33

[1]	Bailey T L, Boden M, Buske F A, Frith M, Grant C E, Clementi L, Ren J, Li W W, Noble W S. 2009. MEME SUITE:tools for motif discovery and searching. Nucleic Acids Research, 37:W202-W208.
[2]	Cao Guanhua, Zhang Xingkai, Bai Xu, Bi Yue, Yin Hongwei, Zhang Yun, He Sen. 2022. Analysis of expression characteristics of panax notoginseng cytochrome P 450 enzyme Gene PnCyp450_3 in response to arbuscular mycorrhizal fungal induction. Chinese Herbal Medicine, 53(21):6848-6856. (in Chinese)
	曹冠华, 张兴开, 柏旭, 毕悦, 殷红伟, 张芸, 贺森. 2022. 三七细胞色素P450酶基因PnCyp450_3响应丛枝菌根真菌诱导的表达特性分析. 中草药, 53(21):6848-6856.
[3]	Castanera R, Ruggieri V, Pujol M, Garcia-Mas J, Casacuberta J M. 2020. An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes. Frontiers in Plant Science, 10:18-15.
[4]	Chen C, Chen H, Zhang Y, Thomas H R, Frank M H, He Y, Xia R. 2020. TBtools:An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8):1194-1202.
[5]	Cui Huiting. 2018. Cloning and functional analysis of MtCYP450in Medicago truncatula[M. D. Dissertation]. Beijing: Chinese Academy of Agricultural Sciences. (in Chinese)
	崔会婷. 2018. 蒺藜苜蓿细胞色素P450基因的克隆及功能分析[硕士论文]. 北京: 中国农业科学院.
[6]	Fang Y, Jiang J, Du Q, Luo L, Li X, Xie X. 2021. Cytochrome P 450 superfamily:evolutionary and functional divergence in sorghum(Sorghum bicolor)stress resistance. Journal of Agricultural and Food Chemistry, 69(37):10952-10961.
[7]	Frear D S, Swanson H R, Tanaka F S. 1969. N-demethylation of substituted 3-(phenyl)-1-methylureas:isolation and characterization of a microsomal mixed function oxidase from cotton. Phytochemistry, 8(11):2157-2169.
[8]	Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez, V M, Henaff E, Camara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutierrez S, Blanca J, Canizares J, Ziarsolo P, Gonzalez-Lbeas D, Rodriguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Mele M, Yang L M, Weng Y Q, Navarro A, Marques-Bonet T, Aranda M A, Nuez F, Pico B, Gabaldon T, Ruglielmo G, Guigo R, Casacuberta J M, Arus P, Puigdomenech P. 2012. The genome of melon(Cucumis melo L.). Proceedings of the National Academy of Sciences of the United States of America, 109(29):11872-11877.
[9]	Hansen C C, Nelson D R, Møller B L, Werck-Reichhart D. 2021. Plant cytochrome P 450 plasticity and evolution. Molecular Plant, 14(8):1244-1265.
[10]	He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant, 13(9):1238-1240.
[11]	Higo K, Ugawa Y, Iwamoto M, Higo H. 1998. PLACE:a database of plant cis-acting regulatory DNA elements. Nucleic Acids Research, 26(1):358-359.
[12]	Hu B, Jin J, Guo A Y, Zhang H, Luo J, Gao G. 2015. GSDS 2.0:an upgraded gene feature visualization server. Bioinformatics(Oxford,England), 31(8):1296-1297.
[13]	Kumar S, Stecher G, Tamura K. 2016. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7):1870-1874.
[14]	Li Wanqing, Gao Bo, Yang Jun, Chen Peng, Li Yuhong. 2015. Physiological characteristic analysis of a new leaf color yellow mutant in cucumber. Acta Agriculturae Boreali-Occidentalis Sinica, 24(7):98-103. (in Chinese)
	李万青, 高波, 杨俊, 陈鹏, 李玉红. 2015. 一个新的黄瓜叶色黄化突变体的生理特性分析. 西北农业学报, 24(7):98-103.
[15]	Ling J, Xie X, Gu X, Zhao J, Ping X, Li Y, Yang Y, Mao Z, Xie B. 2021. High-quality chromosome-level genomes of Cucumis metuliferus and Cucumis melo provide insight into Cucumis genome evolution. The Plant Journal, 107(1):136-148.
[16]	Nelson D, Werck-Reichhart D. 2011. A P450-centric view of plant evolution. The Plant Journal, 66(1):194-211.
[17]	Nuñez-Palenius H.G, Gomez-Lim M, Ochoa-Alejo N, Grumet R, Lester G, Cantliffe J D. 2008. Melon fruits:genetic diversity,physiology,and biotechnology features. Critical Reviews in Biotechnology, 28(1):13-55.
[18]	Rao X, Huang X, Zhou Z, Lin X. 2013. An improvement of the 2^-∆∆CTmethod for quantitative real-time polymerase chain reaction data analysis. Biostatistics,Bioinformatics and Biomathematics, 3(3):71-85.
[19]	Reilly S K, Gosai S J, Gutierrez A, Mackay-Smith A, Ulirsch J C, Kanai M, Mouri K, Berenzy D, Kales S, Butler G M, Gladden-Young A, Bhuiyan R M, Stitzel M L, Finucane H K, Sabeti P C, Tewhey R. 2021. Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH. Nature Genetics, 53(8):1166-1176.
[20]	Rudolf J D, Chang C Y, Ma M, Shen B. 2017. Cytochromes P 450 for natural product biosynthesis in Streptomyces:sequence,structure,and function. Natural Product Reports, 34(9):1141-1172.
[21]	Shen C, Li X. 2023. Genome-wide analysis of the P 450 gene family in tea plant(Camellia sinensis)reveals functional diversity in abiotic stress. BMC Genomics, 24(1):535.
[22]	Terry M J, Kendrick R E. 1999. Feedback inhibition of chlorophyll synthesis in the phytochrome chromophore-deficient aurea and yellow-green-2 mutants of tomato. Plant Physiology, 119(1):143-152.
[23]	Vasav A P, Barvkar V T. 2019. Phylogenomic analysis of cytochrome P 450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters. BMC Genomics, 20(1):116.
[24]	Wang D, Zhang Y, Zhang Z., Zhu J, Yu J. 2010. KaKs_Calculator 2.0:a toolkit incorporating gamma-series methods and sliding window strategies. Genomics,Proteomics & Bioinformatics, 8(1):77-80.
[25]	Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Lee T H, Jin H, Marler B, Guo H, Kissinger J C, Paterson A H. 2012. MCScanX:a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40(7):e49.
[26]	Wei K, Chen H. 2018. Global identification,structural analysis and expression characterization of cytochrome P 450 monooxygenase superfamily in rice. BMC Genomics, 19(1):35.
[27]	Yang J, Deng G, Lian J, Garraway J, Niu Y, Hu Z, Yu J, Zhang M. 2020. The Chromosome-scale genome of melon dissects genetic architecture of important agronomic traits. iScience, 23(8):101422.
[28]	Yano R, Ariizumi T, Nonaka S, Kawazu Y, Zhong S, Mueller L, Giovannoni J J, Rose J K C, Ezura H. 2020. Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Communications Biology, 3(1):432.
[29]	Yu J, Tehrim S, Wang L, Dossa K, Zhang X, Ke T, Liao B. 2017. Evolutionary history and functional divergence of the cytochrome P 450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications. BMC Genomics, 18(1):733.
[30]	Zhang H, Li X, Yu H, Zhang Y, Li M, Wang H, Wang D, Wang H, Fu Q, Liu M, Ji C, Ma L, Tang J, Li S, Miao J, Zheng H, Yi H. 2019. A high-quality melon genome assembly provides insights into genetic basis of fruit trait improvement. iScience, 22:16-27.
[31]	Zhang L, Xu X, Badawy S, Ihsan A, Liu Z, Xie C, Wang X, Tao Y. 2020. A review:effects of macrolides on CYP450 enzymes. Current Drug Metabolism, 21(12):928-937.
[32]	Zheng X, Li P, Lu X. 2019. Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants. Journal of Experimental Botany, 70(18):4619-4630.
[33]	Zhu Y C, Yuan G P, Wang Y F, An G L, Li W H, Liu J P, Sun D X. 2022. Mapping and functional verification of leaf yellowing genes in watermelon during whole growth period. Frontiers in Plant Science, 13:1049114.

Identification of Cytochrome P450 Family Genes in Melon and Expression Analysis in Response to Light Intensity

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