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

Abstract

Moso bamboo (Phyllostachys edulis) 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 8,045 differentially expressed genes (DEGs) and 1,053 differentially expressed proteins (DEPs) were identified in our analyses. Gene ontology and KEGG 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 three significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction (PPI) 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.

Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

“…At the same time, moso bamboo forests also have ecological values of water conservation, fertilization, soil improvement, air purification and climate regulation. Moso bamboo is an excellent model plant due to its rapid growth rate during culm development ( Tao et al, 2020 ; Zhao et al, 2018a ). A better understanding of Moso bamboo’s genome and transcriptome has the potential to yield new genetic resources for the improvement of other crop species ( Peng et al, 2013b ; Pan et al, 2017 ; Liu et al, 2019 ).…”

Transcriptome analysis reveals key genes regulating signaling and metabolic pathways during the growth of moso bamboo (Phyllostachys edulis) shoots

“…Thus, these six G2‐like transcription factors may have important regulatory effects on downstream CK‐responsive genes in the early growth period of bamboo shoots. In addition, the ZR content was up‐regulated significantly in the early growth stages of moso bamboo shoots (Figure 8), which further indicates that the CK signaling pathway leads to the early growth by regulating cell division (Tao et al, 2020). However, how G2‐like responds to genes that regulate cell division downstream in the CK signaling pathway still needs to be studied further.…”

“…The color of the line is between 0 and 1, indicating that there is a positive correlation between the two genes. On the contrary, it shows that there is a negative correlation between the two genes in the early growth stages of moso bamboo shoots (Figure 8), which further indicates that the CK signaling pathway leads to the early growth by regulating cell division (Tao et al, 2020). However, how G2-like responds to genes that regulate cell division downstream in the CK signaling pathway still needs to be studied further.…”

Comparative Genomics Reveals Potential Mechanisms of Plant Beneficial Effects of a Novel Bamboo-Endophytic Bacterial Isolate Paraburkholderia sacchari Suichang626

“…Moso bamboo (Phyllostachys edulis) is widely distributed in southern China. The characteristics of stress tolerance, rapid growth, and high quality fibers make moso bamboo an ideal plant both as a carbon sink and for industrial uses (Peng et al, 2013;Huang and Young, 2019;Churkina et al, 2020;Tao et al, 2020;Ye et al, 2020). Bamboo is one of the largest monocots.…”