Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii)

Wenjuan Liu; Yaqi Yi; Jingyi Zhuang; Chang Ge; Yunpeng Cao; Lin Zhang; Meilan Liu

doi:10.7717/peerj.13981

Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii)

PeerJ. 2022 Sep 28:10:e13981. doi: 10.7717/peerj.13981. eCollection 2022.

Authors

Wenjuan Liu^#^{1

2}, Yaqi Yi^#^{1

2}, Jingyi Zhuang^{1

2}, Chang Ge³, Yunpeng Cao^{1

2}, Lin Zhang^{1

2}, Meilan Liu^{1

2}

Affiliations

¹ Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China.
² Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China.
³ School of Urban Design, Wuhan University, Wuhan, Hubei, China.

^# Contributed equally.

Abstract

The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.

Keywords: Flower and seed development; Low temperature; Tissue-specific expression; Tung tree; VfbHLHs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aleurites* / genetics
Flowers
Gene Expression Profiling
Seeds / genetics
Trees / genetics

Grants and funding

This project was supported by the Scientific Research Fund of Hunan Provincial Education Department (grant nos. 19B600), the Changsha Municipal Natural Science Foundation (grant nos. kq2014156), and the Scientific Research and Innovation Project of Hunan Provincial postgraduates (CX20200742). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.