Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells

Shinjiro Ogita,Komaki Inoue,Yasuo Kato,Yukiko Uehara-Yamaguchi,Tetsuya Sakurai,Keiichi Mochida,Taiji Nomura,Takuhiro Yoshida,Kazuo Shinozaki

doi:10.1038/s41598-018-29645-7

Abstract

Highly-lignified culms of bamboo show distinctive anatomical and mechanical properties compared with the culms of other grass species. A cell culture system for Phyllostachys nigra has enabled investigating the alterations in cellular states associated with secondary cell wall formation during its proliferation and lignification in woody bamboos. To reveal transcriptional changes related to lignification in bamboo, we analyzed transcriptome in P. nigra cells treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) and the synthetic cytokinin benzylaminopurine (BA) by RNA-seq analysis. We found that some genes putatively involved in cell wall biogenesis and cell division were up-regulated in response to the 2,4-D treatment, and the induction of lignification by the BA treatment was correlated with up-regulation of genes involved in the shikimate pathway. We also found that genes encoding MYB transcription factors (TFs) show correlated expression patterns with those encoding cinnamyl alcohol dehydrogenase (CAD), suggesting that MYB TFs presumably regulate secondary cell wall formation in the bamboo cells. These findings suggest that cytokinin signaling may regulate lignification in P. nigra cells through coordinated transcriptional regulation and metabolic alterations. Our results have also produced a useful resource for better understanding of secondary cell wall formation in bamboo plants.

Highlights

Bamboo is an ecologically and economically important grass species
From the sequenced mRNAs, we obtained 783 million reads amounting to approximately 78 gigabases in the filtered dataset; 93.22% of these sequences mapped to the P. edulis draft genome (Supplementary Table S1)
We identified 25,443 P. nigra genes significantly expressed in the cells, which are corresponding to the counterparts annotated in the P. edulis draft genome

Summary

Introduction

Bamboo is an ecologically and economically important grass species. It belongs to the largest subfamily, the Bambusoideae, in the grass family (Poaceae)[1,2], which contains more than 1,500 species that are adapted to diverse climates. To elucidate gene regulatory networks involved in these biological phenomena observed in bamboo species, several studies have utilized transcriptome analyses, and identified spatiotemporal expressions of genes explored across different tissues and developmental stages[6,7,8,9], which improved the understanding of the molecular mechanisms underlying the development and growth in bamboo. These analyses provided little information at the cellular level, and did not identify the molecular mechanisms of cellular differentiation associated with its highly-lignified culm formation. We used RNA-seq based transcriptome analysis to obtain an overview of the gene expression of cultured P. nigra cells, rpc00047, and sought to identify the key pathways and transcription factors involved in its lignification process

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Conclusion