Genomic Identification, Evolutionary Insights and Expression Profiles of AP2 Transcription Factors in Camelina sativa under Heat Stress at Flowering Stage
Aug 2026· Integrative Plant Biotechnology· Vol 4, pp. 177-193· 0 citations· 42 references
TL;DR
A broad characterization of the AP2 gene family in C. sativa using bioinformatics approaches advances the understanding of AP2 family genes in C. sativa, highlighting their evolutionary and regulatory mechanisms.
Abstract
Camelina sativa (False Flax) is a flowering plant that belongs to the family Brassicaceae. It is cultivated as an oilseed crop in Europe and North America. The AP2 transcription factor gene family plays a role in the regulation of biological processes related to growth and development and to the response to environmental and biotic stimuli. AP2 domain is characterized by 2 highly conserved 60 to 70 amino acid long amino acid residues. In Camelina sativa, AP2 family genes have not yet been identified. In our study, we performed a broad characterization of the AP2 gene family in C. sativa using bioinformatics approaches. We identified and retrieved genes containing the AP2 domain in their sequence using both the Plant Transcription Factor Database (Plant TFDB) and the National Center of Biotechnology Information (NCBI). The results of chromosomal localization revealed that 70 AP2 genes in C. sativa were distributed unevenly throughout the genome, indicating the allohexaploid ancestry of the species. Multiple sequence alignment was done by CLUSTALW. CsAP2 proteins were divided into three groups by phylogenetic analysis with and without the 18 A. thaliana AP2 homologs. Gene structure analysis revealed that CsAP2 genes have 0 to 10 introns and some genes lack 5’ or 3’ UTRs or both. Motif analysis revealed that smaller motifs are more conserved in CsAP2 genes of C. sativa. Domain analysis revealed that there are 4 domains in CsAP2 genes, but the most conserved domains across all AP2 genes are the AP2 and the AP2 superfamily. Circos analysis identifies the gene duplication events during the evolution of CsAP2 genes. Synteny analysis fetched out the percentage identity and the homologous gene pair. CAAT-box and TATA-box are the most conserved cis-regulatory elements among CsAP2 genes, and the AAAC-motif, AT-rich sequence, chsCMA2b, chs-Unit 1 m1, DRE, GATT-motif, GTGGC-motif, MSA-like, and the WUN-motif are the least conserved cis-regulatory elements among CsAP2 genes. Expression analysis shows no effect of heat stress on 6 CsAP2 genes and the down regulation of activity of 37 CsAP2 genes and the up regulation of 27 CsAP2 genes. Collectively, this study advances our understanding of AP2 family genes in C. sativa, highlighting their evolutionary and regulatory mechanisms.
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SUMOylation is a well-conserved post-translational modification that is essential for modulating plant adaptation to various abiotic stresses. Although the functions of small ubiquitin-like modifier (SUMO) genes have been reported in various plant species, systematic studies focusing on the SUMO gene family members in alfalfa remain limited. In this study, we identified 49 MsSUMO genes from the alfalfa genome using bioinformatics approaches, and conducted comprehensive analyses of their phylogenetic relationships, structural features, cis-regulatory elements, and expression patterns. Most MsSUMO genes were predicted to localize in the nucleus and cytoplasm, consistent with their roles in transcriptional regulation and protein modification. Phylogenetic analysis grouped MsSUMO, soybean and Arabidopsis SUMO genes into seven subfamilies, which exhibited both high homology and species-specific divergence, suggesting functional differentiation during evolution. Conserved motif and domain analyses revealed strong structural consistency among MsSUMO members, with relatively simple gene architectures. In total, 59 types of cis-elements were detected in the promoter regions, playing crucial roles in plant growth, light signaling, and responses to biotic and abiotic stresses. Abscisic acid-responsive elements (ABREs) were the most abundant, implying that this gene family may serve key functions in stress regulation via the abscisic acid (ABA) signal pathway. Protein interaction network analysis indicated that MsSUMO members cooperate with core enzymes to modulate downstream stress-responsive targets. Transcriptome and real-time quantitative polymerase chain reaction (RT-qPCR) results showed that eight MsSUMO genes exhibited significant expression responses to salt, drought, and waterlogging stresses. Remarkably, six genes consistently exhibited upregulation across all three stress conditions. This observation underscores their potential as pivotal players in abiotic stress tolerance and identifies them as promising candidates for subsequent functional characterization.
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The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays essential roles in growth and development. Chili pepper, as a representative member of the Solanaceae family, is an important vegetable crop with enormous economic value. In this study, using the recently released gap-free telomere-to-telomere genome assembly of pepper, we re-annotated the AP2/ERF transcription factor family and identified 155 high-confidence members. Phylogenetic analysis classified these genes into five subfamilies: AP2 (19), ERF (82), DREB (51), RAV (1), and Soloist (2). Comprehensive analyses of gene structure, conserved motifs, chromosomal distribution, collinearity, cis-elements, and expression profiles revealed substantial structural conservation and functional diversification within the family. Expression profiling highlighted CaBBM, a key member of the AP2 subfamily, as a candidate developmental regulator, prompting further functional characterization. Expression analyses using qRT-PCR and promoter–GUS assays showed that CaBBM was preferentially expressed in stamens, while subcellular localization assays confirmed its nuclear localization. Preliminary analysis of biological functions suggests that heterologous expression of CaBBM in Arabidopsis can lead to phenotypes such as shorter primary roots, smaller leaves and floral organs, and decreased pollen number. In addition, yeast two-hybrid screening identified 12 candidate interacting proteins. These results provide a comprehensive framework for understanding the AP2/ERF family in chili pepper and lay a foundation for elucidating the function and regulatory mechanisms of CaBBM.
