CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
BMC Genomics. 2022 Sep 13;23(1):650. doi: 10.1186/s12864-022-08871-4.
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.
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.
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.
作为植物中最大的转录因子家族之一，AP2/ERF 基因超家族在植物生长、发育、果实成熟以及生物和非生物胁迫反应中发挥重要作用。尽管猕猴桃基因组研究取得了巨大进展，但对猕猴桃的 AP2/ERF 基因的研究甚少。不断增加的猕猴桃基因组资源使我们能够在全基因组范围内揭示猕猴桃 AP2/ERF 基因的组织表达谱。
在本研究中，共鉴定出 A. eriantha 中的 158 个 AP2/ERF 基因。所有基因都可以映射到 29 条染色体上。基于完整蛋白质序列的系统发育分析将它们分为四个主要亚家族。此外，我们的结果表明，相同的亚家族包含相似的基因结构和保守基序。Ka/Ks 计算表明，AP2/ERF 基因家族经历了强烈的纯化选择，进化速度较慢。RNA-seq 显示，AP2/ERF 基因在不同的花发育阶段表达不同，三个对照中 56 个基因被认为是 DEGs。此外，qRT-PCR 表明部分基因表达也有显著差异，表明它们可能是 A. eriantha 花发育的关键调控因子。此外，两个基因（AeAP2/ERF061、AeAP2/ERF067）基于转录组具有丰富的转录水平，这表明它们可能在植物花发育调控和花组织形成中发挥关键作用。
我们鉴定了 AP2/ERF 基因，并展示了它们在两种猕猴桃相关物种 A. eriantha 和 A. chinensis 中的基因结构、保守基序和系统发育关系，以及它们在 A. eriantha 花发育中的潜在作用。这些信息将为进一步鉴定参与猕猴桃花发育的 AP2/ERF 基因的功能奠定基础。
