Identification, characterization and functional differentiation of the NACgene family and its roles in response to cold stress in ginseng, Panax ginsengC.A. Meyer.

Qian Liu,Chunyu Sun,Yanfang Wang,Yi Wang,Jiazhuang Han,Meiping Zhang,Jing Chen,Mingzhu Zhao,Li Li,Kangyu Wang,Yong Pyo Lim

doi:10.1371/journal.pone.0234423

Abstract

The NAC gene family is one of the important plant-specific transcription factor families involved in variety of physiological processes. It has been found in several plant species; however, little is known about the gene family in ginseng, Panax ginseng C.A. Meyer. Here we report identification and systematic analysis of this gene family in ginseng. A total of 89 NAC genes, designated PgNAC01 to PgNAC89, are identified. These genes are alternatively spliced into 251 transcripts at fruiting stage of a four-year-old ginseng plant. The genes of this gene family have five conserved motifs and are clustered into 11 subfamilies, all of which are shared with the genes of the NAC gene families identified in the dicot and monocot model plant species, Arabidopsis and rice. This result indicates that the PgNAC gene family is an ancient and evolutionarily inactive gene family. Gene ontology (GO) analysis shows that the functions of the PgNAC gene family have been substantially differentiated; nevertheless, over 86% the PgNAC transcripts remain functionally correlated. Finally, five of the PgNAC genes, PgNAC05-2, PgNAC41-2, PgNAC48, PgNAC56-1, and PgNAC59, are identified to be involved in plant response to cold stress, suggesting that this gene family plays roles in response to cold stress in ginseng. These results, therefore, provide new insights into functional differentiation and evolution of a gene family in plants and gene resources necessary to comprehensively determine the functions of the PgNAC gene family in response to cold and other abiotic stresses in ginseng.

Highlights

Plants often suffer from a variety of adverse environments, such as salt, drought, cold, pathogens, and insect pests, due to their sessile lifestyle [1]
When the 251 transcripts were aligned to three ginseng databases, with criteria of alignment length 200 nucleotides or amino acids, identity 90%, and e-value 1.0E-06, 105 (42%) of them were aligned to the ginseng cv
The network consisted of 17 clusters, 226 transcript nodes and 1,935 transcript-transcript co-expression edges (Fig 8A). These PgNAC transcripts were much more likely to form a co-expression network than the transcripts randomly selected from Database A in both number of nodes (Fig 8B) and number of edges (Fig 8C). These results indicated that the gene members of the PgNAC gene family functionally differentiated, but they were still functionally correlated in ginseng

Summary

Introduction

Plants often suffer from a variety of adverse environments, such as salt, drought, cold, pathogens, and insect pests, due to their sessile lifestyle [1]. These biotic and abiotic stresses directly or indirectly affect plant growth and development, influencing plant production. To cope with these various environmental stresses, plants have evolved a series of defense mechanisms. Comprehensive dissection of NAC gene family in Panax ginseng. JJKH20200320KJ), and the Development and Reform Commission of Jilin Province (2016C064 and 2018C047-3)

Methods

Results

Conclusion