Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

Abstract

The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

“…The number of AP2/ERF genes was greatest on chromosome 2 (22), chromosome 16 had the fewest (5), and the number on the other chromosomes ranged from 7 to 21. Most of the genes were on both ends of the chromosomes, which was similar to studies in Arabidopsis and other species [ 5 , 32 , 33 ]. The distribution similarity of genes on chromosomes indicates functional consistency.…”

“…Analyzing the exon-intron structure of the JmAP2/ERF gene revealed that 64 members of this family possessed introns, including 27 JmAP2 genes, 2 JmRAV genes, 4 JmSoloist genes, 9 JmDREB genes, and 22 JmERF genes. Among them, the JmAP2 subfamily contained more introns than other families; however, zero or few introns were observed in the JmERF and JmDREB subfamilies; similar results have been found in C. olitorius L. [ 12 ], A. hypogaea L. [ 32 ], and C. illinoinensis [ 33 ]. This seemed to be related to the 122 pairs of segmental duplication events in this study and further confirmed that segmental duplication leads to intron loss with a higher probability than gain [ 36 ].…”

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

“…It is widely known that ancestral species have intron-rich genes, and most plant species have experienced extensive loss or insertion of introns due to selection pressure [ 33 ]. Our results show that almost all AP2 and Soloist subfamily genes of ramie, like in other plant species [ 20 , 32 , 34 ], had introns, whereas most DREB and ERF subfamily genes (71.3%) were intronless. Nevertheless, the RAV subfamily genes in ramie, unlike other plants, all have introns except BnRAV-04 .…”

Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan (Carya illinoinensis) Resistance to Pestalotiopsis microspora

“…The yield and quality of pecan are strongly affected by various biotic and abiotic stresses, such as salt [ 3 , 4 ], drought [ 5 ], and pathogens [ 6 ]. Among the wound pathogens, black spot is a fungal disease caused by Pestalotiopsis microspora , which leads to decayed pecan fruits [ 2 ].…”