Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha

Abstract

Background: As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis.

Results: In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming.

Conclusions: We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.

Keywords: AP2/ERF; Comparative genomics; Expression analysis; Flower development; Kiwifruit; Phylogenetic analysis.

Fig. 1

Flower tissues of A. eriantha sampled for RNA-seq. Stage 1: flower buds; stage 2: unopened flowers; stage 3: full-opening flowers

Fig. 2

The phylogenetic tree of 347 AP2/ERF genes from two kiwifruit species. Different color represents different subfamily. Red pentacle means the bootstrap value

Fig. 3

Gene structures and distributions of conserve motifs of AP2/ERF genes in different subfamilies in A. eriantha. A The phylogenetic tree of AP2/ERF genes in A. eriantha (left); Motifs contained in AP2/ERF proteins (middle) and the exon-intron structures of kiwifruit AP2/ERF genes (right). B Protein sequences of conserved motifs identified in A. eriantha. Red pentacle means the bootstrap value (20–100%)

Fig. 4

The schematic representations for the distributions of AP2/ERF genes in A. eriantha

Fig. 5

Synteny analysis of AP2/ERF gene family in three species. Red line represented the collinear gene pairs in AP2/ERF gene family. Chr represents the different chromosome in A. eriantha. LG represents the different chromosome in A. chinensis. At represents the different chromosome in A. thaliana. Synteny analysis of AP2/ERF gene family within A. eriantha (A), between A. eriantha and A. chinensis (B), between A. eriantha and A. thaliana (C)

Fig. 6

Distribution of the synonymous substitution rate (Ks) between A. eriantha and A. chinensis

Fig. 7

Expression profiles of AeAP2/ERFs. A The expression profile of AeAP2/ERF genes in the kiwifruit at different flower developmental stages. B The expression profiles of different expression genes in the three contrasts. C Venn diagram of DEGs in three combinations. D The relative expressions of several AeAP2/ERF genes analyzed by qRT-PCR. *: P < 0.05; **: P < 0.01; ***: P < 0.001. The colors blue and red correspond to low and high values of gene expression