Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)

Peiqi Ye; Xiaoliang Che; Yang Liu; Ming Zeng; Wenbing Guo; Yongbin Long; Tianyi Liu; Zhe Wang

doi:10.7717/peerj.17388

PeerJ (May 2024)

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)

Peiqi Ye,
Xiaoliang Che,
Yang Liu,
Ming Zeng,
Wenbing Guo,
Yongbin Long,
Tianyi Liu,
Zhe Wang

Affiliations

Peiqi Ye: Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
Xiaoliang Che: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
Yang Liu: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
Ming Zeng: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
Wenbing Guo: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
Yongbin Long: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
Tianyi Liu: Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
Zhe Wang: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China

DOI: https://doi.org/10.7717/peerj.17388
Journal volume & issue: Vol. 12
p. e17388

Abstract

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The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Published in PeerJ

ISSN: 2167-8359 (Online)
Publisher: PeerJ Inc.
Country of publisher: United States
LCC subjects: Medicine; Science: Biology (General)
Website: https://peerj.com/

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