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 AP2/ERF gene family of Chinese willow (Salix matsudana), 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 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified depending on the recently produced whole genome sequencing data of Salix matsudana. These genes were renamed according to the chromosomal location of the SmAP2/ERF genes. The SmAP2/ERF 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 SmAP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from Populus trichocarpa and Salix purpurea showed that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Evolution analysis on paralog gene pairs suggested that progenitor of S. matsudana 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 SmAP2/ERF genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.
Highlights
APETALA 2/ethylene-responsive element binding factors (AP2/ERF) transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses
By Hidden Markov Model (HMM) profile search against the Salix matsudana protein database, a total of 364 full-length AP2/ERF family proteins containing at least one AP2/ERF domain were identified as AP2/ERF superfamily members of Salix matsudana (Fig. 1)
Basing on multiple sequence alignments of 48 AP2/ERF proteins from Arabidopsis and Populus trichocarpa with known categories and 364 Salix matsudana AP2/ERF proteins, we constructed a phylogenetic tree using the neighbor-joining method to explore the phylogenetic relationships of Salix matsudana AP2/ERF proteins
Summary
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, including model plants, horticulture plants, crops, and trees. All of the members of this superfamily possess AP2 domains and, according to the number and structure of AP2 domains, the superfamily is divided into several categories, including AP2, ERF, RAV, and Soloist [1]. Most of the AP2 gene family members have two AP2 domains and can be further divided into AP2 and ANT groups; ERF family members have only one AP2 domain and can be subdivided into ERF and DREB subfamilies based on binding motifs in the promoter of downstream genes. Members of the ERF and DREB subfamilies are classified into 12 groups (groups A1–B6).
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