Abstract

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

Highlights

  • Plants are subjected to numerous biotic and abiotic stresses all time through their growth and development

  • The sequences of 342 APETALA2/Ethylene Responsive Factor (AP2/ERF) gene transcripts downloaded from the Ginseng Genome Database were aligned with 397 transcripts identified in this study with identity 95%, alignment length 200 bp

  • The remaining 51 (27%) PgERF genes whose sequences were quite different from the Korean ginseng AP2/ERF genes were considered as newly discovered AP2/ERF genes in ginseng (S1 Fig and S3 Table)

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Summary

Introduction

Plants are subjected to numerous biotic and abiotic stresses all time through their growth and development. Based on the number and amino acid sequence similarities of the AP2 domains, the AP2/ERF family is divided into the DREB (dehydration responsive element binding), ERF, AP2, RAV (Related to ABI3/VP1) and Soloist subfamilies [6,7]. The members of the ERF subfamily typically bind to the cis-acting element GCC-box and are involved in the signaling pathways of plant hormone, e.g., ethylene (ET), SA, jasmonic acid (JA) and abscisic acid (ABA), and play an important role in both plant growth and development and response to stresses [19,20,21]. The DREB subfamily recognizes the conserved CCGAC motif of the dehydration-responsive element present in stress-responsive genes and is associated with plant response to abiotic stresses [22,23,24]

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