Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo

Tao, Gui-Yun; Ramakrishnan, Muthusamy; Vinod, Kunnummal Kurungara; Yrjälä, Kim; Satheesh, Viswanathan; Cho, Jungnam; Fu, Ying; Zhou, Mingbing

Abstract

Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein–protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.

Citation

Tao, G., Ramakrishnan, M., Vinod, K. K., Yrjälä, K., Satheesh, V., Cho, J., …Zhou, M. (2020). Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo. Tree Physiology, 40(11), 1487-1508. https://doi.org/10.1093/treephys/tpaa090

• Journal Article Type: Article
• Acceptance Date: Jul 9, 2020
• Online Publication Date: Jul 24, 2020
• Publication Date: Oct 29, 2020
• Deposit Date: Nov 21, 2023
• Journal: Tree Physiology
• Print ISSN: 0829-318X
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 40
• Issue: 11
• Pages: 1487-1508
• DOI: https://doi.org/10.1093/treephys/tpaa090
• Keywords: Plant Science; Physiology
• Public URL: https://durham-repository.worktribe.com/output/1945521