杨梅（Myrica rubra）AP2/ERF 基因家族的全基因组鉴定、结构特征和表达谱分析。

Genome-wide identification, structural characterization and expression profiling of AP2/ERF gene family in bayberry (Myrica rubra).

机构信息

Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China.

出版信息

BMC Plant Biol. 2024 Nov 28;24(1):1139. doi: 10.1186/s12870-024-05847-2.

DOI:10.1186/s12870-024-05847-2

PMID:39604860

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11603639/

Abstract

BACKGROUND

Bayberry is the most economically significant fruit within the Myricaceae family, having high nutritional and medicinal value. The AP2/ERF family is a class of transcription factors found mainly in plants. However, the bayberry AP2/ERF gene family has not previously been studied.

RESULTS

In this study, 113 members of the bayberry AP2/ERF gene family were identified. According to the phylogenetic tree, the members of this group are divided into three subfamilies, namely AP2, ERF, and DREB. The gene structure and conserved motifs were analyzed. Chromosome localization showed that 95 genes were unevenly distributed on 8 chromosomes and 18 genes were located on the skeleton. Gene collinearity analysis of the bayberry AP2/ERF gene family showed 12 segmental duplication events, involving 21 AP2/ERFs. In addition, we further investigated the evolutionary relationship of the AP2/ERF gene family between bayberry and six other species. It was found that bayberry was most closely related to Populus trichocarpa and Malus pumila, with 153 and 141 homologous gene pairs, respectively. Cis-acting elements indicated that AP2/ERFs were related to phytohormone responses, light response, abiotic and biotic stress tolerance. Transcriptomic data showed that the expression pattern of AP2/ERF gene was different in bayberry space electric field treatment and at different stages of fruit development. The results of GO annotation revealed the biological processes, cellular component and molecular function that the AP2/ERF genes were involved. And KEGG enrichment analysis indicated that these genes were mainly clustered in genetic information processing and metabolism pathways.

CONCLUSIONS

The AP2/ERF gene was identified in the genome of bayberry, and its structure, conserved motif, and phylogenetic relationship were analyzed. These findings of this study serve as a reference for the genome-wide identification of the AP2/ERF gene family in other species and groundwork for future research on the function of AP2/ERF genes in bayberry.

摘要

背景

杨梅是杨梅科中经济价值最高的果实，具有很高的营养价值和药用价值。AP2/ERF 家族是一类主要存在于植物中的转录因子。然而，杨梅的 AP2/ERF 基因家族尚未被研究过。

结果

在这项研究中，鉴定了杨梅的 113 个 AP2/ERF 基因家族成员。根据系统发育树，该组的成员分为三个亚家族，即 AP2、ERF 和 DREB。对基因结构和保守基序进行了分析。染色体定位表明，95 个基因不均匀分布在 8 条染色体上，18 个基因位于骨架上。杨梅 AP2/ERF 基因家族的基因共线性分析表明，有 12 个片段重复事件，涉及 21 个 AP2/ERFs。此外，我们进一步研究了杨梅和其他六种物种的 AP2/ERF 基因家族之间的进化关系。结果发现，杨梅与毛白杨和苹果的亲缘关系最近，分别有 153 和 141 个同源基因对。顺式作用元件表明，AP2/ERFs 与植物激素反应、光反应、非生物和生物胁迫耐受有关。转录组数据表明，AP2/ERF 基因在杨梅空间电场处理和果实发育不同阶段的表达模式不同。GO 注释的结果揭示了 AP2/ERF 基因参与的生物过程、细胞成分和分子功能。KEGG 富集分析表明，这些基因主要聚集在遗传信息处理和代谢途径中。