Genome-Wide Identification and Analysis of the NAC Transcription Factor Gene Family in Garden Asparagus (Asparagus officinalis)

Caifeng Li; Jingyang Zhang; Qianqian Zhang; Ang Dong; Qiuhong Wu; Xingyu Zhu; Xuli Zhu

doi:10.3390/genes13060976

Genome-Wide Identification and Analysis of the NAC Transcription Factor Gene Family in Garden Asparagus (Asparagus officinalis)

Genes (Basel). 2022 May 30;13(6):976. doi: 10.3390/genes13060976.

Authors

Caifeng Li¹, Jingyang Zhang², Qianqian Zhang¹, Ang Dong¹, Qiuhong Wu¹, Xingyu Zhu¹, Xuli Zhu^{1

3

4

5}

Affiliations

¹ Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
² Tandon School of Engineering, New York University, New York, NY 11201, USA.
³ National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
⁴ Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Ministry of Education, Beijing 100083, China.
⁵ The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China.

Abstract

As a large plant-specific gene family, the NAC (NAM, ATAF1/2, and CUC2) transcription factor is related to plant growth, development, and response to abiotic stresses. Although the draft genome of garden asparagus (Asparagus officinalis) has been released, the genome-wide investigation of the NAC gene family is still unavailable. In this study, a total of 85 A. officinalis NAC genes were identified, and a comprehensive analysis of the gene family was performed, including physicochemical properties, phylogenetic relationship, chromosome localization, gene structure, conserved motifs, intron/exon, cis-acting elements, gene duplication, syntenic analysis, and differential gene expression analysis. The phylogenetic analysis demonstrated that there were 14 subgroups in both A. officinalis and Arabidopsis thaliana, and the genes with a similar gene structure and motif distribution were clustered in the same group. The cis-acting regulatory analysis of AoNAC genes indicated four types of cis-acting elements were present in the promoter regions, including light-responsive, hormone-responsive, plant-growth-and-development-related, and stress-responsive elements. The chromosomal localization analysis found that 81 NAC genes in A. officinalis were unevenly distributed on nine chromosomes, and the gene duplication analysis showed three pairs of tandem duplicated genes and five pairs of segmental duplications, suggesting that gene duplication is possibly associated with the amplification of the A. officinalis NAC gene family. The differential gene expression analysis revealed one and three AoNAC genes that were upregulated and downregulated under different types of salinity stress, respectively. This study provides insight into the evolution, diversity, and characterization of NAC genes in garden asparagus and will be helpful for future understanding of their biological roles and molecular mechanisms in plants.

Keywords: Asparagus officinalis; NAC transcription factor; gene duplication; gene family; genome-wide analysis; salinity stress; syntenic analysis.

Publication types

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

MeSH terms

Arabidopsis* / genetics
Asparagus Plant* / genetics
Asparagus Plant* / metabolism
Gene Expression Profiling
Gene Expression Regulation, Plant
Phylogeny
Plant Proteins / genetics
Plant Proteins / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Plant Proteins
Transcription Factors

Grants and funding

This research was funded by Fundamental Research Funds for the Central Universities (NO. BLX201912) and China Postdoctoral Science Foundation (2019M660496).