In silico analysis of NAC gene family in the mangrove plant Avicennia marina provides clues for adaptation to intertidal habitats

• Published in: Plant molecular biology Vol. 111; no. 4-5; pp. 393 - 413
• Main Authors: Song, Shiwei, Ma, Dongna, Xu, Chaoqun, Guo, Zejun, Li, Jing, Song, Lingyu, Wei, Mingyue, Zhang, Ludan, Zhong, You-Hui, Zhang, Yu-Chen, Liu, Jing-Wen, Chi, Bingjie, Wang, Jicheng, Tang, Hanchen, Zhu, Xueyi, Zheng, Hai-Lei
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.03.2023; Springer; Springer Nature B.V
• Subjects: Adaptation; Avicennia - chemistry; Avicennia - genetics; Avicennia - metabolism; Avicennia marina; Biochemistry; Biomedical and Life Sciences; Coastal ecosystems; Conserved sequence; DNA binding proteins; Ecosystem; Evolutionary genetics; Genes; Genes, Plant; Genetic transcription; Genomes; Genomics; Habitats; Intertidal environment; Life Sciences; Mangroves; Nucleotide sequence; Phylogeny; Plant genetics; Plant growth; Plant Pathology; Plant Sciences; Regulatory sequences; Salt gland; Transcription factors; Transcription Factors - metabolism; Transcriptomes; Function; Evolution; NAC transcription factors; Intertidal habitats; Avicennia marina
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-023-01333-9

NAC (NAM, ATAF1/2, CUC2) transcription factors (TFs) constitute a plant-specific gene family. It is reported that NAC TFs play important roles in plant growth and developmental processes and in response to biotic/abiotic stresses. Nevertheless, little information is known about the functional and evolutionary characteristics of NAC TFs in mangrove plants, a group of species adapting coastal intertidal habitats. Thus, we conducted a comprehensive investigation for NAC TFs in Avicennia marina , one pioneer species of mangrove plants. We totally identified 142 NAC TFs from the genome of A. marina . Combined with NAC proteins having been functionally characterized in other organisms, we built a phylogenetic tree to infer the function of NAC TFs in A. marina . Gene structure and motif sequence analyses suggest the sequence conservation and transcription regulatory regions-mediated functional diversity. Whole-genome duplication serves as the driver force to the evolution of NAC gene family. Moreover, two pairs of NAC genes were identified as positively selected genes of which AmNAC010/040 may be imposed on less constraint toward neofunctionalization. Quite a few stress/hormone-related responsive elements were found in promoter regions indicating potential response to various external factors. Transcriptome data revealed some NAC TFs were involved in pneumatophore and leaf salt gland development and response to salt, flooding and Cd stresses. Gene co-expression analysis found a few NAC TFs participates in the special biological processes concerned with adaptation to intertidal environment. In summary, this study provides detailed functional and evolutionary information about NAC gene family in mangrove plant A. marina and new perspective for adaptation to intertidal habitats. Key message This study provides comprehensive functional and evolutionary information for NAC transcription factor in the genome of mangrove plants Avicennia marina and new perspectives from the regulatory mechanisms for adaptation to intertidal habitats.