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. 2019 Dec 24;20(Suppl 25):687.
doi: 10.1186/s12859-019-3261-z.

Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

Yulian Jiao  1   2 , Qiutao Hu  1 , Yan Zhu  3 , Longfei Zhu  1 , Tengfei Ma  1 , Haiyong Zeng  1 , Qiaolu Zang  1 , Xuan Li  4 , Xinchun Lin  5   6
Affiliations

Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)

Yulian Jiao et al. BMC Bioinformatics. .

Abstract

Background: Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear.

Results: In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo.

Conclusions: This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.

Keywords: Flowering; Phyllostachys violascens; Plant hormone signal transduction; RNA-seq; Stress responsive, MADS box.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The reproductive and vegetative bud samples of Lei bamboo. a-c The flowering buds sampled on March 8th, March 29th and April 12th are named as TF_1, TF_2 and TF_3 respectively. d-f Vegetative buds sampled on March 8th, March 29th and April 12th are named TV_1, TV_2 and TV_3 respectively. g The same rhizome of flowering and non-flowering plants
Fig. 2
Fig. 2
The functional analysis of total unigenes in Lei bamboo. a GO functional classification (b) KEGG classification
Fig. 3
Fig. 3
The venn diagram of differentially expressed genes (DEGs) in Lei bamboo. a the DEGs in TV stages (b) the DEGs in TF stages (c) the DEGs between TF and TV stages
Fig. 4
Fig. 4
The heatmap of the selected DEGs in Lei bamboo flowering (a). the genes involved in plant hormone signaling pathway (b) the genes involved in photoperiod and stress resistance
Fig. 5
Fig. 5
The heatmap of the selected DEGs involved in floral organ development of Lei bamboo
Fig. 6
Fig. 6
Phylogenetic analysis of MADS-box proteins in Arabidopsis and Lei bamboo. a A total of 25 open reading frame sequences in Lei bamboo and 103 proteins in Arabidopsis was used to construct the neighbor-joining Tree. b A total of 25 open reading frame sequences in Lei bamboo and 103 proteins in Arabidopsis was used to construct the maximum likelihood tree
Fig. 7
Fig. 7
The heatmap of the MADs genes belong to ABCDE model in Lei bamboo
Fig. 8
Fig. 8
Quantitative real-time RT-PCR confirmation of 12 candidate genes at the six stages
See this image and copyright information in PMC

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