Dataset Information

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.

SUBMITTER: Song Q

PROVIDER: S-EPMC7714060 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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

Song Qi Q Bari Amna A Li Huan H Chen Ling-Ling LL

FEBS open bio 20201108 12

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. Mos ...[more]

PMID: 32986930

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Project description:Background APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide. Results A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3?h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum. Conclusions In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

Project description:BackgroundThe AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although AP2/ERFs have been thoroughly characterized in many plant species, little is known about this family in the model plant Brachypodium distachyon, especially those involved in the regulatory network of stress processes.ResultsIn this study, a comprehensive genome-wide search was performed to identify AP2/ERF gene family in Brachypodium and a total of 141 BdAP2/ERFs were obtained. Phylogenetic analysis classified them into four subfamilies, of which 112 belonged to ERF, four to RAV and 24 to AP2 as well as one to soloist subfamily respectively, which was in accordance with the number of AP2 domains and gene structure analysis. Chromosomal localization, gene structure, conserved protein motif and cis-regulatory elements as well as gene duplication events analysis were further performed to systematically investigate the evolutionary features of these BdAP2/ERF genes. Furthermore, the regulatory network between BdAP2/ERF and other genes were constructed using the orthology-based method, and 39 BdAP2/ERFs were found to be involved in the regulatory network and 517 network branches were identified. The expression profiles of BdAP2/ERF during development and under diverse stresses were investigated using the available RNA-seq and microarray data and ten tissue-specific and several stress-responsive BdAP2/ERF genes were identified. Finally, 11 AP2/ERF genes were selected to validate their expressions in different tissues and under different stress treatments using RT-PCR method and results verified that these AP2/ERFs were involved in various developmental and physiological processes.ConclusionsThis study for the first time reported the characteristics of the BdAP2/ERF family, which will provide the invaluable information for further evolutionary and functional studies of AP2/ERF in Brachypodium, and also contribute to better understanding the molecular basis for development and stresses tolerance in this model species and beyond.

Dataset Information

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

Publications

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

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