Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour
- We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan.. - Results: A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. - This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement.. - The AP2/ERF superfamily is one of the largest transcrip- tion factor families in plants. - The functions of the AP2/ERF superfamily members have been studied widely in plants and are known to regulate diverse developmental processes and stress re- sponses. - Thus, genome-wide identification of the AP2/ERF superfamily members have been conducted in many plants, such as Arabidopsis thaliana [1], soybean (Glycine max) [25], barley (Hordeum vulgare) [26], grape (Vitis vinifera) [27], poplar (Populus trichocarpa) [28], Chinese cabbage (Brassica rapa ssp. - The longan genome was sequenced in our laboratory, which provides a great opportunity for the genome-wide study of the AP2/ERF superfamily [33]. - This study provides valuable clues for functional characterization of the AP2/ERF super- family in longan.. - Identification of the AP2/ERF superfamily in longan All candidate AP2/ERF genes corresponding to the Pfam AP2 domain (PF00847) were extracted from the longan genome dataset [33]. - lengths of the coding sequence (CDS), protein sequence, protein isoelectric point (pI) and molecular weight (Add- itional file 1: Table S1). - Phylogenetic analysis and classification of the longan AP2/ERF superfamily. - The motif analysis showed that in Dlo_002336.1 (ERF-91), Dlo_000247.1 (ERF-2) and Dlo_000250.1 (ERF-3), the highly conserved AP2 domain was similar to that of the DREB family (Fig. - Motif composition and gene structure of the longan AP2/. - ERF superfamily. - We identified a total of 30 motifs and used them to analyze the charac- teristics of the DlAP2/ERF superfamily proteins (Fig. - AP2/ERF superfamily genes. - The different SNPs of the AP2/ERF superfamily mem- bers indicate the genetic diversity and could be used to develop variety-specific genetic markers.. - a Gnen ID list of the DlAP2/ERF superfamily.. - 3 Predicted cis-acting elements in the promoter of the DlAP2/ERF superfamily. - The four transcriptome datasets included the NEC and embryogenic cultures (EC, IcpEC, and GE) of the ‘HHZ’ cultivar, the ECs. - treatments, and nine organs of the ‘SJM’ cultivar. - We first analyzed the transcriptional levels of the AP2/ERF genes in the NEC and embryogenic cultures of the ‘HHZ’ cultivar (Fig. - 1 The SNP numbers of the AP2/ERF superfamily detected in the NEC and embryogenic cultures of ‘ HHZ ’ cultivar. - 2 The SNP numbers of the AP2/ERF superfamily detected in the EC under different light quality treatments. - 3 The SNP numbers of the AP2/ERF superfamily detected in the EC under different hormone treatments. - 4 The SNP numbers of the AP2/ERF superfamily detected in nine organs of ‘ SJM ’ clutivar. - 5 The InDel numbers of the AP2/ERF superfamily detected in. - 1 The InDel numbers of the AP2/ERF superfamily detected in the NEC and embryogenic cultures of ‘ HHZ ’ cultivar. - 2 The InDel numbers of the AP2/ERF superfamily detected in the EC under different light quality treatments. - 3 The InDel numbers of the AP2/ERF superfamily detected in the EC under different hormone treatments. - 4 The InDel numbers of the AP2/ERF superfamily detected in nine organs of ‘ SJM ’ clutivar. - 6 The AS events of the AP2/ERF superfamily detected in different tissues and in response to different treatments. - a The AS events of the AP2/ERF superfamily detected in the NEC and embryogenic cultures of ‘ HHZ ’ cultivar. - b The AS events of the AP2/ERF superfamily detected in the EC under different light quality treatments. - c The AS events of the AP2/ERF superfamily detected in the EC under different hormone treatments. - d The AS events of the AP2/ERF superfamily detected in nine organs of ‘ SJM ’ clutivar. - To investigate whether the AP2/ERF superfamily re- sponds to 2,4-D and KT, the expression levels of the DlAP2/ERF genes in the transcriptome dataset from hor- mone treatments (2,4-D and KT) were analyzed. - 7 The AS events of the DlAP2/ERF genes detected in different tissues and in response to different treatments. - We also analyzed the transcriptional levels of DlAP2/ERF genes in nine organs of the ‘SJM’ cultivar (Additional file 14:. - Some of the genes were specifically expressed in dif- ferent organs. - To confirm the transcriptional regulation of the DlAP2/. - ERF genes in the NEC and embryogenic cultures of the. - We found that some of the DlAP2/ERF genes were significantly induced by multiple. - Members of the AP2/ERF superfamily have been identified in many species whose genomes have been se- quenced . - In this study, we identified 125 members of the AP2/ERF superfamily in the longan gen- ome, including 101 ERF, 19 AP2, four RAV family mem- bers, and one Soloist. - The motif analysis of the DlAP2/ERF superfamily showed that most of the AP2/ERF superfamily members contained motif-1, motif-2, motif-3, and motif-4 related to the AP2 domain. - Although some motifs of the AP2/ERF superfamily were highly conserved, the unique motifs in different groups may have important functions in longan. - the ‘HHZ’ cultivar, and nine organs of the ‘SJM’ cultivar.. - Up to now, few reports on changes in AS events of the AP2/ERF superfamily genes are available. - Besides, Dlo_000287.1 (AP2), Dlo_015581.1 (RAP2.7), and Dlo_009234.2 (RAP2.7) also showed high numbers of AS events in multiple organs of the ‘SJM’ culti- var. - AGL15, and may act upstream of the AIL branch. - Tissue-specific expression profiles indicated that most of the DlAP2/ERF genes were expressed in almost all or- gans (96. - Overall, these findings provide insights into the poten- tial functional roles of the AP2/ERF superfamily mem- bers. - The SNPs between the ‘HHZ’ and ‘SJM’ cultivars were diverse and provided valuable insights into the evolutionary characteristics of the longan AP2/ERF superfamily. - Phylogenetic analysis, sequence analysis, and cis -acting elements in the promoters of members of the. - longan AP2/ERF superfamily. - SNPs, InDels, and AS events analyses of the longan AP2/. - Details of the cis-acting elements identified in this study.. - The SNP annotation of the DlAP2/ERF superfamily detected in ‘ HHZ ’ and ‘ SJM ’ clutivars. - a The SNP annotation of the DlAP2/ERF superfamily detected in the NEC and embryogenic cultures (EC, IcpEC and GE) of ‘ HHZ ’ cultivar. - b The SNP annotation of the DlAP2/ERF superfamily detected in the EC under light quality (blue, white, and dark as the control) treatments. - c The SNP annotation of the DlAP2/ERF superfamily detected in the EC under hormone (2,4-D and KT) treatments. - d The SNP annotation of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivar.. - The InDel annotation of the DlAP2/ERF superfamily detected in ‘ HHZ ’ and ‘ SJM ’ clutivars. - a The InDel annotation of the DlAP2/ERF superfamily detected in the NEC and embryogenic cultures of ‘ HHZ ’ cultivar. - b The InDel annotation of the DlAP2/ERF superfamily detected in the EC under light quality treatments. - c The InDel annotation of the DlAP2/ERF superfamily detected in the EC under hormone treatments. - d The InDel annotation of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivar.. - The alternative splicing events of the DlAP2/. - a The alternative splicing events (alternative 3 ′ splice site acceptor) of the DlAP2/ERF superfamily detected in the NEC and embryogenic cultures of. - b The alternative splicing events (5 ′ splice site donor) of the DlAP2/ERF superfamily detected in the NEC and embryogenic cultures of. - c The alternative splicing events (intron retention) of the DlAP2/ERF superfamily detected in the NEC and embryogenic cultures of. - d The alternative splicing events (exon skipping) of the. - The alternative splicing events of the DlAP2/ERF superfamily detected in the EC under light quality treatments.. - a The alternative splicing events (alternative 3 ′ splice site acceptor) of the DlAP2/ERF superfamily detected in the EC under light quality treatments.. - b The alternative splicing events (5 ′ splice site donor) of the DlAP2/ERF superfamily detected in the EC under light quality treatments. - c The alternative splicing events (intron retention) of the DlAP2/ERF superfamily detected in the EC under light quality treatments. - d The alternative splicing events (exon skipping) of the DlAP2/ERF superfamily detected in the EC under light quality treatments.. - The alternative splicing events of the DlAP2/ERF superfamily detected in the EC under hormone treatments. - a The alternative splicing events (alternative 3 ′ splice site acceptor) of the DlAP2/ERF superfamily detected in the EC under hormone treatments. - b The alternative splicing events (5 ′ splice site donor) of the DlAP2/ERF superfamily detected in the EC under hormone treatments. - c The alternative splicing events (intron retention) of the DlAP2/ERF superfamily detected in the EC under hormone treatments. - d The alternative splicing events (exon skipping) of the DlAP2/ERF superfamily detected in the EC under hormone treatments.. - The alternative splicing events of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivars. - a The alternative splicing events (alternative 3 ′ splice site acceptor) of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivars. - b The alternative splicing events (5 ′ splice site donor) of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivars. - c The alternative splicing events (intron retention) of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivars. - d The alternative splicing events (exon skipping) of the DlAP2/ERF superfamily detected in nine organs of ‘ SJM ’ cultivars.. - a RNA-seq data of the DlAP2/ERF superfamily used in this study. - Genome-wide analysis of the ERF gene family in Arabidopsis and Rice. - The Arabidopsis thaliana At4g13040 gene, a unique member of the AP2/. - Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. - Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. - Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. - Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica).. - Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers. - Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response. - Genome-wide analysis of the AP2/. - Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum). - Complexity of the alternative splicing landscape in plants
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