Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple ( <i>Ananas comosus</i> (L.) Merr.)

Abstract

Pineapple (<i>Ananas comosus</i> (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 <i>ERF</i> genes <i>(AcoERFs</i>) were identified in pineapple genome, named from <i>AcoERF1</i> to <i>AcoERF74</i>, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of <i>AcoERFs</i>, and the <i>AcoERFs</i> within the same group possess similar gene structures and motif compositions. Three genes (<i>AcoERF71</i>, <i>AcoERF73</i> and <i>AcoERF74</i>) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and <i>cis</i>-elements analysis of <i>ERF</i> genes provided deep insight into the evolution and function of pineapple <i>ERF</i> genes. Furthermore, we analyzed the expression profiling of <i>AcoERF</i> in different tissues and developmental stages, and 22 <i>AcoERF</i> genes were expressed in all examined tissues, in which five genes (<i>AcoERF13</i>, <i>AcoERF16</i>, <i>AcoERF31</i>, <i>AcoERF42</i>, and <i>AcoERF65</i>) had high expression levels. Additionally, nine <i>AcoERF</i> genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.