Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow ( <i>Salix matsudana</i> )

Abstract

AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the <i>AP2/ERF</i> gene family of Chinese willow (<i>Salix matsudana</i>), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. In this study, 364 <i>AP2/ERF</i> genes of <i>Salix matsudana</i> (<i>SmAP2/ERF</i>) were identified depending on the recently produced whole genome sequencing data of <i>Salix matsudana</i>. These genes were renamed according to the chromosomal location of the <i>SmAP2/ERF</i> genes. The <i>SmAP2/ERF</i> genes included three major subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members) and two Soloist genes. Genes' structure and conserved motifs were analyzed in SmAP2/ERF family members, and introns were not found in most genes of the ERF subfamily, some unique motifs were found to be important for the function of <i>SmAP2/ERF</i> genes. Syntenic relationships between the <i>SmAP2/ERF</i> genes and <i>AP2/ERF</i> genes from <i>Populus trichocarpa</i> and <i>Salix purpurea</i> showed that <i>Salix matsudana</i> is genetically more closely related to <i>Populus trichocarpa</i> than to <i>Salix purpurea</i>. Evolution analysis on paralog gene pairs suggested that progenitor of <i>S. matsudana</i> originated from hybridization between two different diploid salix germplasms and underwent genome duplication not more than 10 Mya. RNA sequencing results demonstrated the differential expression patterns of some <i>SmAP2/ERF</i> genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in <i>Salix matsudana</i>.