Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>)
The ethylene-responsive element (<i>AP2/ERF</i>) 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 <i>AP2/ERF</i> genes were identified from the pecan geno...
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/6/2920 |
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| author | Bingbing Yang Xiaohua Yao Yanru Zeng Chengcai Zhang |
| author_facet | Bingbing Yang Xiaohua Yao Yanru Zeng Chengcai Zhang |
| author_sort | Bingbing Yang |
| collection | DOAJ |
| description | The ethylene-responsive element (<i>AP2/ERF</i>) 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 <i>AP2/ERF</i> genes were identified from the pecan genome and renamed according to the chromosomal distribution of the <i>CiAP2/ERF</i> genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 <i>AP2</i>, 168 <i>ERF</i>, six <i>RAV</i>, and two <i>Soloist</i> 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 <i>AP2/ERF</i> genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of <i>AP2/ERF</i>s. The expression profiling of 202 <i>CiAP2/ERF</i> 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 <i>AP2/ERF</i> 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. |
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| spelling | doaj.art-870a28fbd071485fbd677b5f0fbb7b4f2023-11-24T01:29:10ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01236292010.3390/ijms23062920Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>)Bingbing Yang0Xiaohua Yao1Yanru Zeng2Chengcai Zhang3The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, ChinaThe Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, ChinaState Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, ChinaThe Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, ChinaThe ethylene-responsive element (<i>AP2/ERF</i>) 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 <i>AP2/ERF</i> genes were identified from the pecan genome and renamed according to the chromosomal distribution of the <i>CiAP2/ERF</i> genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 <i>AP2</i>, 168 <i>ERF</i>, six <i>RAV</i>, and two <i>Soloist</i> 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 <i>AP2/ERF</i> genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of <i>AP2/ERF</i>s. The expression profiling of 202 <i>CiAP2/ERF</i> 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 <i>AP2/ERF</i> 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.https://www.mdpi.com/1422-0067/23/6/2920ethylene-responsive elements (ERF)pecan (<i>Carya illinoinensis</i>)RNA-SeqERF-VII |
| spellingShingle | Bingbing Yang Xiaohua Yao Yanru Zeng Chengcai Zhang Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) International Journal of Molecular Sciences ethylene-responsive elements (ERF) pecan (<i>Carya illinoinensis</i>) RNA-Seq ERF-VII |
| title | Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) |
| title_full | Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) |
| title_fullStr | Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) |
| title_full_unstemmed | Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) |
| title_short | Genome-Wide Identification, Characterization, and Expression Profiling of <i>AP2/ERF</i> Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (<i>Carya illinoinensis</i>) |
| title_sort | genome wide identification characterization and expression profiling of i ap2 erf i superfamily genes under different development and abiotic stress conditions in pecan i carya illinoinensis i |
| topic | ethylene-responsive elements (ERF) pecan (<i>Carya illinoinensis</i>) RNA-Seq ERF-VII |
| url | https://www.mdpi.com/1422-0067/23/6/2920 |
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