Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots

Abstract

Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. The present study identified a total of 58,652 genes and 150 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild-type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis ‘Pachyloen’) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 14,029 (65.17%) differentially expressed genes (DEGs) and 68 (45.33%) differentially expressed miRNAs (DEmiRs) were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations, each between two successive stages (WTS2/TWS2_vs_WTS1/TWS1, WTS3/TWS3_vs_WTS2/TWS2, WTS4/TWS4_vs_WTS3/TWS3, and WTS5/TWS5_vs_WTS4/TWS4), and the WTTW group was composed of five combinations, each between two relative stages (TWS1–5_vs_WTS1–5). Additionally, among the phytohormones, zeatin (ZT) showed more remarkable changes in concentrations than indole-3-acetic acid (IAA), gibberellic acid (GA3), and abscisic acid (ABA) throughout the five stages in the WT and the TW groups. Moreover, 125 cleavage sites were identified for 387 miRNA-mRNA pairs via degradome sequencing (P < 0.05). The dual-luciferase reporter assay confirmed that 13 miRNAs bound to 12 targets. Fluorescence in situ hybridization (FISH) localized miR166 and miR160 in the shoot apical meristem (SAM) and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.

Combined omics unravels the molecular mechanism of golden-leaf coloration in Koelreuteria paniculata ‘jinye’

“…4c), were predicted. Further, analyses were carried out to identify whether these interactions were either coherent (the expression level of target mRNA is more when that of miRNA is less; the “DU” and “UD” patterns) or non-coherent (miRNA and its target mRNA have similar expression profiles) (Li et al ., 2022).…”

Transcriptome Analysis to Identify Genes Related to Flowering Reversion in Tomato

“…Inflorescence meristems were collected in each of the above three periods three times in each experimental group from both cultivars. The samples were extracted and purified according to the method of Li et al [ 75 ]. GA3 (B20187), IAA (B21810) and 6-BA (B24213) standards from Sigma (Yuanye Bio-Technology Co., Ltd., Shanghai, China) were used in these analyses.…”

The miR166–mRNA network regulates vascular tissue differentiation in Moso bamboo

“…The transcriptome, small RNA, and degradome sequencing data of underground shoot samples of WT and the TW Moso bamboo at the WTS1/TWS1-WTS5/TWS5 stages were downloaded from the NCBI SRA database using the accession No. PRJNA753616 (https://www.ncbi.nlm.nih.gov/Traces/study/ ?acc=PRJNA753616) (Li et al, 2022).…”

“…miRNAs have also been identified in Frontiers in Genetics frontiersin.org the aboveground parts of mature bamboo culms (Ge et al, 2017). miRNAs have been shown to play an important role in the tissue differentiation of underground shoots at stages S1-S5 in wildtype (WT) Moso bamboo and its thick-walled (TW) variant (P. edulis "Pachyloen"), and miR166s are located in the vascular tissues of Moso bamboo shoots (Li et al, 2022). However, the roles of miR166s in the aforementioned regulatory network remain unclear; furthermore, little is known about their function in vascular tissue differentiation in bamboo seedlings.…”

“…Here, we aimed to 1) identify the target genes of miR166s, 2) study the interplay between miR166s and their targets, 3) characterize the localization of miR166s in bamboo shoots and seedlings, and 4) evaluate the implications of localization differences for tissue differentiation. We performed an integrated analysis of miR166s with the transcriptome, miRNAome, and degradome sequencing data using underground shoot samples of the WT Moso bamboo and the TW variant P. edulis "Pachyloen" taken throughout five stages of development (WTS1/ TWS1-WTS5/TWS5) (Li et al, 2022). We also performed dual-luciferase reporter assays to study the interplay between miR166s and their predicted targets and RNA fluorescence in situ hybridization (FISH) to determine the localization of miR166s in leaf, root, and internode samples collected from two-month-old bamboo seedlings (Figure 1F).…”