Identification and analysis of micro‐exons in AP2/ERF and MADS gene families

Abstract

Micro-exons are a set of ultrashort exons with lengths ≤ 51 nucleotides. Our previous study revealed that micro-exons were enriched in AP2 domains and K-box domains, which are crucial components of AP2/ERF (APETALA2/ethylene-responsive element-binding protein) and MADS-box (an acronym of MCM1, AGAMOUS, DEFICIENS and SRF) genes, respectively. In this study, we analyzed micro-exons in the AP2/ERF family from 63 species and demonstrated that 76.8% of micro-exons are concentrated in AP2 domains. Most micro-exons appeared in the AP2 subfamily of all the terrestrial plants, but not algae. In addition, micro-exons and AP2 domains are conserved and under negative selection. The MIKC gene is a typical MADS-box gene family in terrestrial plants and includes one MADS-box domain and one K-box domain. A total of 92.3% of micro-exons were observed in K-box domains, and two micro-exons usually encoded a region of K-box domain, which is the key to MADS-box protein polymerization. Furthermore, the micro-exons of the K-box domain had higher ratios of nonsynonymous mutations than those of the AP2 domains. Overall, here we explored the relationships and differences among micro-exons in AP2/ERF and MADS families, and revealed potential functional roles of micro-exons in these domains.

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

“…88% of micro-exons were contributed by the AP2 subfamily in the sesame pan-genome with only 15 out of 128 identified genes lacking micro-exons. Song et al, 2020, also reported that AP2 micro-exon genes are highly conserved which we found only to be partially true in the pan-genome. 44% of micro-exon genes were conserved in the pan-genome in the AP2 sub-family whereas the extent was higher in the Chinese accessions particularly in landraces Baizhima and Mishouzhima, wherein 83% sequence conservation was observed.…”

“…The exonic fragments of length <51bp were classified as microexons (Song et al, 2020) and we found 227 micro-exons in the sesame pan-genome varying in size from 3bp to 50 bp (SI-3A, SI-3B, SI-4 and SI-6). AP2/ERF gene family had 195 micro-exons distributed along 133 genes with Swetha contributing a major share of 36.…”

“…A similar trend was found in the case of micro-exons wherein family-wise difference was quite wider with AP2/ERF family having more micro-exons than WRKY. The AP2/ERF family was reported to be micro-exon rich (Song et al, 2020) and in the sesame pangenome, micro-exons totaled 10% of total exons as against 1.96% in the WRKY family. 88% of micro-exons were contributed by the AP2 subfamily in the sesame pan-genome with only 15 out of 128 identified genes lacking micro-exons.…”

“…Micro-exons of size ≤15bp are considered as shortest and interestingly 38% of WRKY microexons belonged to this category whereas in the AP2/ERF family only 9% of micro-exons fulfilled this criterion (Yu et al, 2022). The most common micro-exons occurring in AP2/ERF genes are of sizes 9, 26, 31, and 45 bp according to Song et al, 2020. In sesame, the most common micro-exon is 50 bp occurring in 54% of AP2 genes at exonic positions 4, 5 or 6. An estimated 35% of AP2 genes without the 50bp micro-exon contained two micro exons of 25 and 30 bp size, occurring together at 2 nd and 3 rd exons in the same order.…”

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

“…It was observed that A1, A4, and A5 classes are more closely related, while A2 and A6 classes shared a combined clade due to the same conserved motifs. The AP2 domain consists of one alpha helix made up of 18 amino acids that assist in the interactions of DREB genes with other proteins, followed by three antiparallel beta sheets on the major groove of the DNA ( Song et al., 2020 ). The identified 20 motifs in the Sl DREB sequences have a variable composition that is the possible reason for the classification of DREB genes into different classes with high structural resemblance with the AP2 domain.…”