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Open AccessArticle

An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’

by Zhiquan Wang 1,2, Jianfeng Hua 1,2, Yunlong Yin 1,2, Chunsun Gu 1,2, Chaoguang Yu 1,2, Qin Shi 1,2, Jinbo Guo 1,2, Lei Xuan 1,2,* and Fangyuan Yu 3,*
1
Jiangsu Engineering Research Center for Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
2
Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
3
Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(5), 1225; https://doi.org/10.3390/ijms20051225
Received: 30 January 2019 / Revised: 2 March 2019 / Accepted: 7 March 2019 / Published: 11 March 2019
(This article belongs to the Special Issue Root Development in Plants)
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation. View Full-Text
Keywords: adventitious root formation; morphology; proteome; Taxodium; transcriptome adventitious root formation; morphology; proteome; Taxodium; transcriptome
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Wang, Z.; Hua, J.; Yin, Y.; Gu, C.; Yu, C.; Shi, Q.; Guo, J.; Xuan, L.; Yu, F. An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’. Int. J. Mol. Sci. 2019, 20, 1225.

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