Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.).

Tingting Li,Ying Liu,Xiaoyu Wu,Wenqiu Pan,Fei Wang,Licao Cui,Yiyuan Yuan,Yihan Li

doi:10.3389/fpls.2021.684619

Abstract

Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.

Highlights

One of the major differences between eukaryotes and prokaryotes is that the former has organelles, while the latter does not (Quesada, 2016)
The updated reference genome of barley, Morex v2, provided invaluable resources for HvmTERF identification, and a total of 60 mitochondrial transcription termination factor (mTERF) genes were identified in barley using a combined method (Supplementary Tables 4, 5)
The significantly lower nucleotide diversity loss passing from wild barley accessions to landraces in this study indicated that the HvmTERF gene family might have suffered simple bottleneck effects, rather than selection, in the process of barley domestication

Summary

Introduction

One of the major differences between eukaryotes and prokaryotes is that the former has organelles, while the latter does not (Quesada, 2016). Thousands of proteins have been predicted to be localized in plant mitochondria and chloroplasts according to bioinformatics analysis, most of which are encoded by the nuclear genome (Binder and Brennicke, 2003; Huang et al, 2013; Lee et al, 2013). The organellar gene expression (OGE) apparatus is a precisely coordinated system that largely depends on a great many of proteins encoded by nuclear genes (Pfannschmidt et al, 2015; Quesada, 2016). Three different polymerases involved in the transcriptional machinery have been demonstrated, including a multi-subunit plastid-encoded RNA polymerase (PEP) and two single-subunit nucleus-encoded RNA polymerases (NEPs) (Pfannschmidt et al, 2015). Currently known auxiliary factors can only partially explain the transcriptional machinery, suggesting the existence of additional unidentified regulatory factors that are required for organellar gene transcription (Kühn et al, 2007; Liere et al, 2011)

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Discussion

Conclusion