Genomic Identification, Evolutionary Insights and Expression Profiles of AP2 Transcription Factors in Camelina sativa under Heat Stress at Flowering Stage
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.