Transcriptome analysis of genes involved in flower and leaf color of Oncidium by RNA-seq
Ma-Yin Wang
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0009-0001-7707-9031
Yu Ding
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0000-0001-7803-0806
Ye Zhang
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0009-0000-2575-0025
Lu Sun
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0009-0007-7062-8636
Xi-Qiang Song
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0000-0001-7690-707X
Dai-Cheng Hao
Hainan Boda Orchid Technology Co. Ltd, Haikou 570311, Chinahttps://orcid.org/0009-0001-6811-8334
Wei-Shi Li
Hainan Boda Orchid Technology Co. Ltd, Haikou 570311, Chinahttps://orcid.org/0009-0009-9095-4732
Min-Qiang Tang
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, ChinaPeng Ling
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, ChinaShang-Qian Xie
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, Chinahttps://orcid.org/0000-0002-8590-1814
Abstract
Oncidium, an important tropical orchid, has high ornamental value due to its specific color and occupies a significant market position for the worldwide flower. Transcriptome analysis of flower and leaf color formation provides new sources for producing novel Oncidium hybridum cultivars. We sequenced 12 samples of flowers (yellow and white) and leaves (striped and regular) of O. hybridum and assembled 381,136 and 453,566 unigene sequences from RNA-seq data, respectively. Among unigenes, 662 and 1,324 differentially expressed genes were identified in flower and leaf samples, respectively. Gene ontology and pathway enrichment showed that secondary metabolite biosynthetic pathways were responsible for flower and leaf color formation. It was determined that UGT75C1, E2.4.1.115, CCD7, E2.1.1.76, and CCoAOMT are involved in regulating flower color, and UGT75C1, LHCB, UGT, RP-L18Ae, and ABCB1 play crucial roles in regulating leaf color. Kyoto Encyclopedia of Genes and Genomes analysis revealed that UGT75C1 was significantly enriched in the anthocyanin biosynthetic pathway, showing effects on flower and leaf colors. This study was the first detailed analysis of the molecular mechanisms of O. hybridum flower and leaf colors, and the results advanced the understanding of the genetic basis of flower and leaf colors; they also provided additional support for improving commercial value and producing novel cultivars of O. hybridum.
Keywords:
Oncidium hybridum, RNA-seq, differential analysis, differentially expressed genes, key genesReferences
Adjei, M.O., Luo, J., Li, X., Du, J., Luan, A., Li, S., Ma, J. (2023). Function of ALA content in porphyrin metabolism regulation of Ananas comosus var. bracteatus. Int. J. Mol. Sci., 24(6), 5274. https://doi.org/10.3390/ijms24065274 DOI: https://doi.org/10.3390/ijms24065274
Andrews, S. (2014). FastQC a quality control tool for high throughput sequence data. Babraham Bioinforma. Available: https://www.bioinformatics.babraham.ac.uk/projects/fastqc [date of access: 6.07.2022].
Cai, W., Zhang, D., Zhang, X., Chen, Q., Liu, Y., Lin, L., Xiang, L., Yang, Y., Xu, L., Yu, X., Li, Y. (2023). Leaf color change and photosystem function evaluation under heat treatment revealed the stress resistance variation between Loropetalum chinense and L. chinense var. rubrum. Peer J., 11, e14834. https://doi.org/10.7717/peerj.14834 DOI: https://doi.org/10.7717/peerj.14834
Chang, Y.L., Huang, L.M., Kuo, X.Z., Chen, Y.Y., Lin, S.T., Jeng, M.F., Yeh, H.H., Tsai, W.C., Chen, H.H. (2023). PbABCG1 and PbABCG2 transporters are required for the emission of floral monoterpenes in Phalaenopsis bellina. Plant J., 114(2), 279–292. https://doi.org/10.1111/tpj.16133 DOI: https://doi.org/10.1111/tpj.16133
Chen, X., Mao, X., Huang, J., Yang, D., Wu, J., Dong, S., Lei, K., Ge, G., Li, C.Y., Wei, L. (2011). KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res., 39(S2), W316–W322. https://doi.org/10.1093/nar/gkr483 DOI: https://doi.org/10.1093/nar/gkr483
Chiou, C.Y., Yeh, K.W. (2008). Differential expression of MYB gene (OgMYB1) determines color patterning in floral tissue of Oncidium Gower Ramsey. Plant Molecular Biol., 66(4), 379–388. https://doi.org/10.1007/s11103-007-9275-3 DOI: https://doi.org/10.1007/s11103-007-9275-3
Fitter, D.W., Martin, D.J., Copley, M.J., Scotland, R.W., Langdale, J.A. (2010). GLK gene pairs regulate chloroplast development in diverse plant species. Plant J., 31(6), 713–727. https://doi.org/10.1046/j.1365-313X.2002.01390.x DOI: https://doi.org/10.1046/j.1365-313X.2002.01390.x
Galperin, M.Y., Wolf, Y. I., Makarova, K.S., Vera Alvarez, R., Landsman, D., Koonin, E.V. (2020). Cog database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res., 49(D1), D274–D281. https://doi.org/10.1093/nar/gkaa1018 DOI: https://doi.org/10.1093/nar/gkaa1018
Giordano D., Provenzano S., Ferrandino A., Vitali M., Pagliarani C., Roman F., Cardinale F., Castellarin S.D., Schubert A. (2016). Characterization of a multifunctional caffeoyl-CoA O-methyltransferase activated in grape berries upon drought stress. Plant Physiol. Bioch., 101, 23–32. https://doi.org/10.1016/j.plaphy.2016.01.015 DOI: https://doi.org/10.1016/j.plaphy.2016.01.015
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Amit, I. (2013). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol., 29, 644–652. https://doi.org/10.1038/nbt.1883 DOI: https://doi.org/10.1038/nbt.1883
Hieber, A.D., Mudalige-Jayawickrama, R.G., Kuehnle, A.R. (2006). Color genes in the orchid Oncidium Gower Ramsey: identification, expression, and potential genetic instability in an interspecific cross. Planta, 223(3), 521–531. https://doi.org/10.1007/s00425-005-0113-z DOI: https://doi.org/10.1007/s00425-005-0113-z
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernandez-Plaza, A., Forslund, S.K., Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C., Bork, P. (2019). 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: https://doi.org/10.1093/nar/gky1085
Kim, E.H., Li, X.P., Razeghifard, R., Anderson, J.M., Niyogi, K.K., Pogson, B.J., Chow, W.S. (2009). The multiple roles of light-harvesting chlorophyll a/b-protein complexes define structure and optimize function of Arabidopsis chloroplasts: a study using two chlorophyll b-less mutants. Biochim Biophys Acta., 1787(8), 973–984. https://doi.org/10.1016/j.bbabio.2009.04.009 DOI: https://doi.org/10.1016/j.bbabio.2009.04.009
Liao, L., Li, Y., Lan, X., Yang, Y., Wei, W., Ai, J., Feng, X., Chen, H., Tang, Y., Xi, L., Wang, Z. (2023). Integrative analysis of fruit quality and anthocyanin accumulation of plum cv. ‘Cuihongli’ (Prunus salicina Lindl.) and its bud mutation. Plants (Basel), 12(6), 1357. https://doi.org/10.3390/plants12061357 DOI: https://doi.org/10.3390/plants12061357
Love, M.I., Huber, W., Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8 DOI: https://doi.org/10.1186/s13059-014-0550-8
Niu, Y., Jiang, X.,Xu, X. (2016). Reaserch advances on transcription factor MYB gene family in plant. Mol. Breed., 14(8), 2050–2059. https://doi.org/10.1080/15592324.2019.1613131 DOI: https://doi.org/10.1080/15592324.2019.1613131
Pan, X., Zheng, H., Zhao, J., Xu, Y.,Li, X. (2016). ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating shoot branching. Planta., 243(6), 1407–1418. https://doi.org/10.1007/s00425-016-2479-5 DOI: https://doi.org/10.1007/s00425-016-2479-5
Pan, Y., Bradley, G., Pyke, K., Ball, G., Lu, C., Fray, R., Marshall, A., Jayasuta, S., Baxter, C., Wijk, R.V. (2013). Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol., 161(3), 1476–1485. https://doi.org/10.1104/pp.112.212654 DOI: https://doi.org/10.1104/pp.112.212654
Patra, B., Schluttenhofer, C., Wu, Y., Pattanaik, S., Yuan, L. (2013). Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochim. Biophys. Acta Gene Regul. Mech., 1829(11), 1236–1247. https://doi.org/10.1016/j.bbagrm.2013.09.006 DOI: https://doi.org/10.1016/j.bbagrm.2013.09.006
Patro, R., Duggal, G., Love, M.I., Irizarry, R.A., Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods, 14(4), 417–419. https://doi.org/10.1038/nmeth.4197 DOI: https://doi.org/10.1038/nmeth.4197
Rogalski, M., Ruf, S., Bock, R. (2006). Tobacco plastid ribosomal protein S18 is essential for cell survival. Nucleic Acids Res., 34(16), 4537–4545. https://doi.org/10.1093/nar/gkl634 DOI: https://doi.org/10.1093/nar/gkl634
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-glucosyl-transferase in Freesia hybrida. Plant Cell Rep., 30(7), 1209–1218. https://doi.org/10.1007/s00299-011-1029-7 DOI: https://doi.org/10.1007/s00299-011-1029-7
Wang, Q., Zhu, J., Li, B., Li, S., Yang, Y., Wang, Q., Xu, W., Wang, L. (2023). Functional identification of anthocyanin glucosyltransferase genes: a Ps3GT catalyzes pelargonidin to pelargonidin 3-O-glucoside painting the vivid red flower color of Paeonia. Planta., 257(4), 65. https://doi.org/10.1007/s00425-023-04095-2 DOI: https://doi.org/10.1007/s00425-023-04095-2
Yang, L., Gan, C.Y., Wei, M.Q., Zeng, J., Shen, L.J., Su, D.H. (2017). Research advance on cultivation management technology of Oncidium hybridum. J. Green Sci. Technol., 2017(17), 114–118. https://doi.org/10.16663/j.cnki.lskj.2017.17.041
Yue, X.Q., Zhang, Y., Yang, C.K., Li, J.G., Rui, X., Ding, F., Hu, F.C., Wang, X.H., Ma, W.Q., Zhou, K.B. (2022). Genome-wide identification and expression analysis of carotenoid cleavage oxygenase genes in Litchi (Litchi chinensis Sonn.). BMC Plant Biol., 22(1), 394. https://doi.org/10.1186/s12870-022-03772-w DOI: https://doi.org/10.1186/s12870-022-03772-w
Zhang, Q.S. (2022). Analysis of pigment content and photosynthetic characteristics in three leaf color mutants of Pachira glabra. J. Minnan Normal Univ. (Nat. Sci.), 35(3), 97–104. https://doi.org/10.16007/j.cnki.issn2095-7122.2022.03.015
Zhang, X., Zhang, L., Zhang, D., Su, D., Li, W., Wang, X., Chen, Q., Cai, W., Xu, L., Cao, F., Zhang, D., Yu, X., Li, Y. (2023). Comprehensive analysis of metabolome and transcriptome reveals the mechanism of color formation in different leave of Loropetalum Chinense var. Rubrum. BMC Plant Biol., 23(1), 133. https://doi.org/10.1186/s12870-023-04143-9 DOI: https://doi.org/10.1186/s12870-023-04143-9
Zhao, M., Li, X., Zhang, X., Zhang, H.,Zhao, X. (2020). Mutation mechanism of leaf color in plants: a review. Forests, 11(8), 851. https://doi.org/10.3390/f11080851 DOI: https://doi.org/10.3390/f11080851
Zhao, Y., Qi, X., Liu, Z., Zheng, W., Guan, J., Liu, Z., Ren, J., Feng, H., Zhang, Y. (2022). Transcriptome and metabolome profiling to explore the causes of purple leaves formation in non-heading Chinese cabbage (Brassica rapa L. ssp. chinensis Makino var. mutliceps Hort.). Foods, 11(12), 1787. https://doi.org/10.3390/foods11121787 DOI: https://doi.org/10.3390/foods11121787
Zhu, G., Yang, F., Shi, S., Li, D., Wang, Z., Liu, H., Huang, D., Wang, C. (2015). Transcriptome characterization of Cymbidium sinense ‘Dharma’ using 454 pyrosequencing and its application in the identification of genes associated with leaf color variation. PLoS One, 10(6), e0128592. https://doi.org/10.1371/journal.pone.0128592 DOI: https://doi.org/10.1371/journal.pone.0128592
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0009-0001-7707-9031
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0000-0001-7803-0806
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0009-0000-2575-0025
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0009-0007-7062-8636
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0000-0001-7690-707X
Hainan Boda Orchid Technology Co. Ltd, Haikou 570311, China https://orcid.org/0009-0001-6811-8334
Hainan Boda Orchid Technology Co. Ltd, Haikou 570311, China https://orcid.org/0009-0009-9095-4732
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China
Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Horticulture, Hainan University, Haikou 570228, China https://orcid.org/0000-0002-8590-1814
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Articles are made available under the conditions CC BY 4.0 (until 2020 under the conditions CC BY-NC-ND 4.0).
Submission of the paper implies that it has not been published previously, that it is not under consideration for publication elsewhere.
The author signs a statement of the originality of the work, the contribution of individuals, and source of funding.
