Transcriptome analysis of flower colour reveals the correlation between SNP and differential expression genes in Phalaenopsis.
DEGs
Flower color
Phalaenopsis
RNA-seq
SNP mutation
Journal
Genes & genomics
ISSN: 2092-9293
Titre abrégé: Genes Genomics
Pays: Korea (South)
ID NLM: 101481027
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
received:
02
03
2022
accepted:
27
06
2023
medline:
28
11
2023
pubmed:
7
7
2023
entrez:
6
7
2023
Statut:
ppublish
Résumé
Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources. To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study. In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level. The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis. This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.
Sections du résumé
BACKGROUND
BACKGROUND
Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources.
OBJECTIVE
OBJECTIVE
To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study.
METHODS
METHODS
In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level.
RESULTS
RESULTS
The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis.
CONCLUSION
CONCLUSIONS
This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.
Identifiants
pubmed: 37414912
doi: 10.1007/s13258-023-01422-5
pii: 10.1007/s13258-023-01422-5
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1611-1621Subventions
Organisme : National Natural Science Foundation of China
ID : 32060149
Organisme : National Natural Science Foundation of China
ID : 31760316
Informations de copyright
© 2023. The Author(s) under exclusive licence to The Genetics Society of Korea.
Références
Bai L, Chen Q, Jiang L, Lin Y, Ye Y, Liu P, Wang X, Tang H (2019) Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla. Hortic Res 6(1):42. https://doi.org/10.1038/s41438-019-0128-4
doi: 10.1038/s41438-019-0128-4
pubmed: 30854215
pmcid: 6397888
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60. https://doi.org/10.1038/nmeth.3176
doi: 10.1038/nmeth.3176
pubmed: 25402007
Cai J, Liu X, Vanneste K, Proost S, Tsai W-C, Liu K-W, Chen L-J, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao Y-Y, Pan Z-J, Hsu C-C, Yang Y-P, Hsu Y-C, Chuang Y-C, Dievart A, Dufayard J-F, Xu X, Wang J-Y, Wang J, Xiao X-J, Zhao X-M, Du R, Zhang G-Q, Wang M, Su Y-Y, Xie G-C, Liu G-H, Li L-Q, Huang L-Q, Luo Y-B, Chen H-H, Van de Peer Y, Liu Z-J (2015) The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47(1):65–72. https://doi.org/10.1038/ng.3149
doi: 10.1038/ng.3149
pubmed: 25420146
Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X (2015) Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol 16:30. https://doi.org/10.1186/s13059-015-0596-2
doi: 10.1186/s13059-015-0596-2
pubmed: 25723335
pmcid: 4342890
Chen L, Li L, Dai Y, Wang X, Duan Y, Yang G (2015) De novo transcriptome analysis of Osmanthus serrulatus Rehd. Flowers and leaves by Illumina sequencing. Biochem Syst Ecol 61:531–540. https://doi.org/10.1016/j.bse.2015.07.027
doi: 10.1016/j.bse.2015.07.027
Chong X, Zhang F, Wu Y, Yang X, Zhao N, Wang H, Guan Z, Fang W, Chen F (2016) A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the identification of candidate genes in Chrysanthemum. Genome Biol Evol 8(12):3661–3671. https://doi.org/10.1093/gbe/evw270
doi: 10.1093/gbe/evw270
pubmed: 28082602
pmcid: 5521737
Chugh S, Guha S, Rao IU (2009) Micropropagation of orchids: a review on the potential of different explants. Sci Hort 122(4):507–520. https://doi.org/10.1016/j.scienta.2009.07.016
doi: 10.1016/j.scienta.2009.07.016
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152. https://doi.org/10.1093/bioinformatics/bts565
doi: 10.1093/bioinformatics/bts565
pubmed: 23060610
pmcid: 3516142
Gao LW, Jiang DH, Yang YX, Li YX, Sun GS, Ma ZH, Zhang CW (2016) De novo sequencing and comparative analysis of two Phalaenopsis orchid tissue-specific transcriptomes. Russ J Plant Physiol 63(3):391–400. https://doi.org/10.1134/s1021443716020072
doi: 10.1134/s1021443716020072
Gomez C, Conejero G, Torregrosa L, Cheynier V, Ageorges A (2011) In vivo grapevine anthocyanin transport involves vesicle-mediated trafficking and the contribution of ANTHOMATE transporters and GST. Plant J 67(6):960–970
doi: 10.1111/j.1365-313X.2011.04648.x
pubmed: 21605207
Griesbach RJ, Janick J, Whipkey A (2002) Development of Phalaenopsis orchids for the mass-market. In: Trends in New Crops & New Uses Fifth National Symposium,
Guo Y, Qiu L-J (2013) Allele-specific marker development and selection efficiencies for both flavonoid 3’-hydroxylase and flavonoid 3’,5’-hydroxylase genes in soybean subgenus soja. Theor Appl Genet 126(6):1445–1455. https://doi.org/10.1007/s00122-013-2063-3
doi: 10.1007/s00122-013-2063-3
pubmed: 23463490
pmcid: 3664743
Holcroft DM, Kader AA (1999) Carbon dioxide–induced changes in color and anthocyanin synthesis of stored strawberry fruit. HortScience 34(7):1244–1248
doi: 10.21273/HORTSCI.34.7.1244
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen Lars J, von Mering C, Bork P (2018) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47(D1):D309–D314. https://doi.org/10.1093/nar/gky1085
doi: 10.1093/nar/gky1085
pmcid: 6324079
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360. https://doi.org/10.1038/nmeth.3317
doi: 10.1038/nmeth.3317
pubmed: 25751142
pmcid: 4655817
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923–930. https://doi.org/10.1093/bioinformatics/btt656
doi: 10.1093/bioinformatics/btt656
pubmed: 24227677
Ling LF, Subramaniam S (2007) Biochemical analyses of Phalaenopsis violacea Orchids. Asian J Biochem 2(4):237–246
doi: 10.3923/ajb.2007.237.246
Lloyd A, Brockman A, Aguirre L, Campbell A, Bean A, Cantero A, Gonzalez A (2017) Advances in the MYB–bHLH–WD repeat (MBW) Pigment Regulatory Model: Addition of a WRKY factor and co-option of an anthocyanin MYB for Betalain Regulation. Plant Cell Physiol 58(9):1431–1441. https://doi.org/10.1093/pcp/pcx075
doi: 10.1093/pcp/pcx075
pubmed: 28575507
pmcid: 5914458
Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali AE, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot M-F, Lacroix V (2016) SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Res 44(19):e148–e148. https://doi.org/10.1093/nar/gkw655
doi: 10.1093/nar/gkw655
pubmed: 27458203
pmcid: 5100560
Luo H, Li W, Zhang X, Deng S, Xu Q, Hou T, Pang X, Zhang Z, Zhang X (2019) In planta high levels of hydrolysable tannins inhibit peroxidase mediated anthocyanin degradation and maintain abaxially red leaves of Excoecaria Cochinchinensis. BMC Plant Biol 19(1):315. https://doi.org/10.1186/s12870-019-1903-y
doi: 10.1186/s12870-019-1903-y
pubmed: 31307378
pmcid: 6632198
Oren-Shamir M (2009) Does anthocyanin degradation play a significant role in determining pigment concentration in plants? Plant Sci 177(4):310–316. https://doi.org/10.1016/j.plantsci.2009.06.015
doi: 10.1016/j.plantsci.2009.06.015
Patra B, Schluttenhofer C, Wu Y, Pattanaik S, Yuan L (2013) Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1829(11):1236–1247. https://doi.org/10.1016/j.bbagrm.2013.09.006
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11(9):1650–1667. https://doi.org/10.1038/nprot.2016.095
doi: 10.1038/nprot.2016.095
pubmed: 27560171
pmcid: 5032908
Pourcel L, Irani NG, Lu Y, Riedl K, Schwartz S, Grotewold E (2010) The formation of Anthocyanic Vacuolar Inclusions in Arabidopsis thaliana and Implications for the sequestration of anthocyanin pigments. Mol Plant 3(1):78–90. https://doi.org/10.1093/mp/ssp071
doi: 10.1093/mp/ssp071
pubmed: 20085894
Reinprecht Y, Perry GE, Peter Pauls K (2017) A Comparison of Phenylpropanoid Pathway Gene Families in Common Bean. Focus on P450 and C4H Genes. In: The Common Bean Genome. Compendium of Plant Genomes. pp 219–261. https://doi.org/10.1007/978-3-319-63526-2_11
Shaipulah NF, Muhlemann JK, Woodworth BD, Van Moerkercke A, Verdonk JC, Ramirez AA, Haring MA, Dudareva N, Schuurink RC (2016) CCoAOMT Down-Regulation activates anthocyanin biosynthesis in Petunia. Plant Physiol 170(2):717–731. https://doi.org/10.1104/pp.15.01646
doi: 10.1104/pp.15.01646
pubmed: 26620524
Su V, Hsu B-D (2003) Cloning and expression of a putative cytochrome P450 gene that influences the colour of Phalaenopsis flowers. Biotechnol Lett 25(22):1933–1939. https://doi.org/10.1023/b:Bile.0000003989.19657.53
doi: 10.1023/b:Bile.0000003989.19657.53
pubmed: 14719829
Sudarsono, Haristianita MD, Handini AS, Sukma D (2017) Molecular marker development based on diversity of genes associated with pigment biosynthetic pathways to support breeding for novel colors inPhalaenopsis. Acta Hort 1167305–312. https://doi.org/10.17660/ActaHortic.2017.1167.44
Sui X, Gao X, Ao M, Wang Q, Yang D, Wang M, Fu Y, Wang L (2011) cDNA cloning and characterization of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in Freesia hybrida. Plant Cell Rep 30(7):1209–1218
doi: 10.1007/s00299-011-1029-7
pubmed: 21318353
Sun H, Guo K, Feng S, Zou W, Li Y, Fan C, Peng L (2015) Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiosperms. Ecol Evol 5(16):3413–3420. https://doi.org/10.1002/ece3.1613
doi: 10.1002/ece3.1613
pubmed: 26380674
pmcid: 4569036
Taguchi G, Imura H, Maeda Y, Kodaira R, Hayashida N, Shimosaka M, Okazaki M (2000) Purification and characterization of UDP-glucose: hydroxycoumarin 7-O-glucosyltransferase, with broad substrate specificity from tobacco cultured cells. Plant Sci 157(1):105–112. https://doi.org/10.1016/s0168-9452(00)00270-3
doi: 10.1016/s0168-9452(00)00270-3
pubmed: 10940474
Tanaka Y, Sasaki N, Ohmiya A (2008) Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. The Plant journal: for cell and molecular biology 54(4):733–749. https://doi.org/10.1111/j.1365-313X.2008.03447.x
doi: 10.1111/j.1365-313X.2008.03447.x
pubmed: 18476875
Tao J, Cao C, Zhao D, Zhou C, Liang G (2010) Molecular analysis and expression of phenylalanine ammonia-lyase from poinsettia (Euphorbia pulcherrima willd). Afr J Biotechnol 10(2):126–135
Tatsuzawa F, Saito N, Seki H, Hara R, Honda T (1997) Acylated cyanidin glycosides in the red-purple flowers of Phalaenopsis. Phytochemistry 45(1):173–177
doi: 10.1016/S0031-9422(96)00802-3
Wang LM, Zhang J, Dong XY, Fu ZZ, Jiang H, Zhang HC (2018) Identification and functional analysis of anthocyanin biosynthesis genes in Phalaenopsis hybrids. Biol Plant 62(1):45–54
doi: 10.1007/s10535-017-0763-2
Wang N, Song G, Zhang F, Shu X, Cheng G, Zhuang W, Wang T, Li Y, Wang Z (2023) Characterization of the WRKY Gene Family related to Anthocyanin Biosynthesis and the Regulation mechanism under Drought stress and Methyl Jasmonate Treatment in Lycoris radiata. Int J Mol Sci 24(3). https://doi.org/10.3390/ijms24032423
Wu Q, Wu J, Li SS, Zhang HJ, Feng CY, Yin DD, Wu RY, Wang LS (2016) Transcriptome sequencing and metabolite analysis for revealing the blue flower formation in waterlily. BMC Genomics 17(1):897. https://doi.org/10.1186/s12864-016-3226-9
doi: 10.1186/s12864-016-3226-9
pubmed: 27829354
pmcid: 5101690
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39:W316–322 (Web Server issue). https://doi.org/10.1093/nar/gkr483
doi: 10.1093/nar/gkr483
pubmed: 21715386
pmcid: 3125809
Yamazaki M, Gong Z, Fukuchi-Mizutani M, Fukui Y, Tanaka Y, Kusumi T, Saito K (1999) Molecular cloning and biochemical characterization of a Novel anthocyanin 5-O-Glucosyltransferase by mRNA Differential Display for Plant Forms regarding anthocyanin. J Biol Chem 274(11):7405–7411
doi: 10.1074/jbc.274.11.7405
pubmed: 10066805
Yan H, Pei X, Zhang H, Li X, Zhang X, Zhao M, Chiang VL, Sederoff RR, Zhao X (2021) MYB-Mediated regulation of Anthocyanin Biosynthesis. Int J Mol Sci 22(6). https://doi.org/10.3390/ijms22063103
Yang IS, Kim S (2015) Analysis of whole transcriptome sequencing data: Workflow and Software. Genomics Inf 13(4):119–125
doi: 10.5808/GI.2015.13.4.119
Yang Y, Sun F, Zhang C (2013) Construction of full-length cDNA Library and the cDNA cloning of F3′H in Phalaenopsis. Acta Bot Boreali-Occidentalia Sinica 33(9):1731–1731
Yang Y, Wang J, Ma Z, Sun G, Zhang C (2014) De novo sequencing and comparative transcriptome analysis of white petals and red labella in Phalaenopsis for discovery of genes related to flower color and floral differentation. Acta Soc Bot Pol 83(3):191–199. https://doi.org/10.5586/asbp.2014.023
doi: 10.5586/asbp.2014.023
Yu G, Wang LG, Han Y, He QY (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16(5):284–287. https://doi.org/10.1089/omi.2011.0118
doi: 10.1089/omi.2011.0118
pubmed: 22455463
pmcid: 3339379
Zhang N, Chen L, Ma S, Wang R, He Q, Tian M, Zhang L (2020) Fine mapping and candidate gene analysis of the white flower gene brwf in chinese cabbage (Brassica rapa L). Sci Rep 10(1):6080–6080. https://doi.org/10.1038/s41598-020-63165-7
doi: 10.1038/s41598-020-63165-7
pubmed: 32269266
pmcid: 7142070
Zhao J, Dixon R, US Department of Agriculture (2010). 2015. Floriculture crops.14 summary. Washington: US Department of Agriculture. The ‘ins’ and ‘outs’ of flavonoid transport Trends Plant Sci 15 (2):72–80. https://doi.org/10.13271/j.mpb.016.004530
Zhao Y, Wang K, Wang W-l, Yin T-t, Dong W-q, Xu C-j (2019) A high-throughput SNP discovery strategy for RNA-seq data. BMC Genomics 20 (1)
Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C (2020) The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. J Exp Bot 71(19):5808–5822. https://doi.org/10.1093/jxb/eraa355
doi: 10.1093/jxb/eraa355
pubmed: 32725154
Zhong HQ, Huang ML, Jian-She WU, Fang RH (2013) Cloning and expression of key enzyme genes involved in Phalaenopsis Anthocyanins synthesis. Fujian Journal of Agricultural Sciences
Zhou X, Li J, Zhu Y, Ni S, Chen J, Feng X, Zhang Y, Li S, Zhu H, Wen Y (2017) De novo Assembly of the Camellia nitidissima Transcriptome reveals key genes of Flower Pigment Biosynthesis. Front Plant Sci 8. https://doi.org/10.3389/fpls.2017.01545