Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba

Xian Zhou,Yongling Liao,Gongping Nie,Shuiyuan Cheng,Soo-Un Kim,Jiabao Ye,Feng Xu,Zexiong Chen

doi:10.1038/s41598-020-69305-3

Abstract

Basic helix–loop–helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In recent years, many bHLH family genes have been identified and characterized in woody plants. However, a systematic analysis of the bHLH gene family has not been reported in Ginkgo biloba, the oldest relic plant species. In this study, we identifed a total of 85 GbbHLH genes from the genomic and transcriptomic databases of G. biloba, which were classified into 17 subfamilies based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon–intron range in GbbHLHs from 0 to 12. The MEME analysis showed that two conserved motifs, motif 1 and motif 2, distributed in most GbbHLH protein. Subcellular localization analysis exhibited that most GbbHLHs located in nucleus and a few GbbHLHs were distributed in chloroplast, plasma membrane and peroxisome. Promoter cis-element analysis revealed that most of the GbbHLH genes contained abundant cis-elements that involved in plant growth and development, secondary metabolism biosynthesis, various abiotic stresses response. In addition, correlation analysis between gene expression and flavonoid content screened seven candidate GbbHLH genes involved in flavonoid biosynthesis, providing the targeted gene encoding transcript factor for increase the flavonoid production through genetic engineering in G. biloba.

Highlights

The basic helix–loop–helix proteins are one of the most important and largest transcription factor families in plants
We identified 85 GbbHLHs through HMMER and BLAST from G. biloba
These GbbHLH genes were classified into 17 subfamilies by comparative phylogenetic analysis with A. thaliana and M. domestica Basic helix–loop–helix (bHLH) proteins

Summary

Introduction

The basic helix–loop–helix (bHLH) proteins are one of the most important and largest transcription factor families in plants. Group C contain bHLH domain and PAS domain that bind ACGTG or GCGTG sequences, which are involved in developmental signaling and environmental homeostasis[12]. Group F contains COE domain except bHLH domain for dimerization and DNA binding, which is related to head development and formation of olfactory sensory n eurons[11]. Flavonoids are synthesized by the combination of the phenylpropanoid and polyketide p athways[16].Transcription factor were involved in flavonoid biosynthesis by regulating expression of structural genes[17]. Our data provided the targeted gene resource of transcript factor involved in flavonoids biosynthesis for increase the flavonoid production through genetic engineering in G. biloba

Methods

Findings

Discussion

Conclusion