Transcriptome profiling of Capsicum annuum using Illumina- and PacBio SMRT-based RNA-Seq for in-depth understanding of genes involved in trichome formation

Shenghua Gao,Chuying Yu,Changxian Yang,Yanxu Yin,Juntawong Niran,Chunhai Jiao,Fei Wang,Ning Li,Minghua Yao

doi:10.1038/s41598-021-89619-0

Abstract

Trichomes, specialized epidermal cells located in aerial parts of plants, play indispensable roles in resisting abiotic and biotic stresses. However, the regulatory genes essential for multicellular trichrome development in Capsicum annuum L. (pepper) remain unclear. In this study, the transcript profiles of peppers GZZY-23 (hairy) and PI246331 (hairless) were investigated to gain insights into the genes responsible for the formation of multicellular trichomes. A total of 40,079 genes, including 4743 novel genes and 13,568 differentially expressed genes (DEGs), were obtained. Functional enrichment analysis revealed that the most noticeable pathways were transcription factor activity, sequence-specific DNA binding, and plant hormone signal transduction, which might be critical for multicellular trichome formation in hairy plants. We screened 11 DEGs related to trichome development; 151 DEGs involved in plant hormone signal transduction; 312 DEGs belonging to the MYB, bHLH, HD-Zip, and zinc finger transcription factor families; and 1629 DEGs predicted as plant resistance genes (PRGs). Most of these DEGs were highly expressed in GZZY-23 or trichomes. Several homologs of trichome regulators, such as SlCycB2, SlCycB3, and H, were considerably upregulated in GZZY-23, especially in the trichomes. The transcriptomic data generated in this study provide a basis for future characterization of trichome formation in pepper.

Highlights

Plant trichomes, small specialized organs originating from epidermal cells, are one of the key factors serving as a buffer zone between the plant surface and the e nvironment[1,2]
The crucial positive transcription factors (TFs) include GLABRA1 (GL1), its functionally equivalent counterparts WEREWOLF (WER) and MYB23, which act as R2R3 type-MYB transcription factors[8,9]; GLABRA3 (GL3), ENHANCER OF GLABRA3 (EGL3), TRANSPARENT TESTA (TT8), and MYC-1, which act as basic helix-loop-helix proteins[10,11,12]; and TRANSPARENT
We found that long macro-trichomes and sporadic short trichomes cover the stem surface of GZZY-23 (Fig. 1B)

Summary

Introduction

Small specialized organs originating from epidermal cells, are one of the key factors serving as a buffer zone between the plant surface and the e nvironment[1,2]. HD-ZIP I transcription factor-encoding gene CsGL1, positively regulates the formation of trichomes and fruit spines in cucumber[31]. The trichomes on pepper leaves, or stems, are highly specialized structures originating from the epidermal cells, and have recently attracted research attention for their effect on biotic and abiotic stress responses in plants. Similar to those in tomato, the trichomes in pepper are multicellular. Previous studies have shown that the pepper trichome locus 1 (Ptl1) is located in the same region as the H (hair) locus in tomato[32,35] These results indicate genetic loci controlling trichome formation is conserved in Solanaceae. Research on pepper trichomes is needed to analyze the mechanism of multicellular trichome formation

Methods

Results

Discussion

Conclusion