New insight into the rapid growth of the Mikania micrantha stem based on DIA proteomic and RNA-Seq analysis

• Published in: Journal of proteomics Vol. 236; p. 104126
• Main Authors: Cui, Can, Wang, Zhen, Su, Yingjuan, Wang, Ting
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.03.2021
• Subjects: Adventitious root; adventitious roots; agroforestry; auxins; carbon dioxide fixation; DIA; energy; gene expression regulation; invasive species; Mikania micrantha; Photosynthetic; plant hormones; proteomics; sequence analysis; signal transduction; Stem; stem elongation; transcription (genetics); Transcriptome; transcriptomics; vegetative propagation; Adventitious root; Mikania micrantha; DIA; Photosynthetic; Stem; Transcriptome
• ISSN: 1874-3919; 1876-7737
• DOI: 10.1016/j.jprot.2021.104126

Mikania micrantha is one of the world's most invasive plants, which causes severe damage to natural ecosystems and agroforestry systems due to its rapid stem growth. This work investigated the proteomic and transcriptomic profiles of M. micrantha in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious roots and primary roots with the final goal of elucidating differentially expressed genes and proteins responsible for the rapid growth of stem. The objective was approached by using DIA-based proteomic and RNA-Seq technologies. More than seven giga-transcriptome clean reads were sequenced, and 5196 protein species were identified. Differentially expressed genes identified in all stem tissues were significantly enriched in photosynthesis and carbon fixation, suggesting that the stem possesses a strong photosynthetic capacity in order to maintain the energy supply for this species. Analysis of differentially expressed proteins showed that proteins related to photosystem I/II and the cytochrome b6/f complex, such as D1, D2, and cp43, were also highly accumulated in the adventitious roots, corroborating the transcriptome analysis results. These results provided basic proteomic and transcriptional expression information about the M. micrantha stem and adventitious root, thereby improving our understanding of the molecular mechanism underlying rapid growth in this species. This is the first study to investigate the proteomic and transcriptomic profiles of Mikania micrantha, a highly invasive plant, in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious and primary roots, using the latest DIA-based (data-independent acquisition mode) proteomic and RNA-Seq technologies. A comprehensive study was carried out, and differentially expressed genes and differentially expressed proteins identified in the pre-internode, post-internode, and internode tissues were significantly enriched during photosynthesis and carbon fixation, suggesting that the M. micrantha stem possesses a strong photosynthetic capacity that allows the plant to maintain a high energy supply. Enriched plant hormone signal transduction pathway analysis revealed an interaction between auxin and other phytohormones involved in adventitious root development. The study provided basic data on the molecular mechanism of M. micrantha vegetative propagation and the rapid growth of its stem. The novel scientific content of this study successfully builds upon the limited information currently available on the subject, therefore warranting publication. [Display omitted] •Mikania micrantha is a highly invasive plant, causing damage due to rapid growth.•Differentially expressed genes in stem tissues were enriched in ‘photosynthesis and carbon fixation’.•Energy metabolism and photosynthetic activities form the basis of Adventitious root development.•Mikania micrantha adventitious root has a strong photosynthetic capacity.•Auxin interacts with other phytohormones involved in adventitious root development.