三种咖啡属植物（卡内弗拉咖啡、尤金尼奥咖啡和阿拉比卡咖啡）AP2/ERF基因家族的全基因组比较特征分析及进化洞察

Comparative genome-wide characterization and evolutionary insights into the AP2/ERF gene family in three Coffea species (C. canephora, C. eugenioides, and C. arabica).

作者信息

Park Sunchung, Ahn Ezekiel, Zhang Dapeng, Meinhardt Lyndel W

机构信息

Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, USA.

出版信息

BMC Genomics. 2025 Jul 11;26(1):653. doi: 10.1186/s12864-025-11850-0.

DOI:10.1186/s12864-025-11850-0

PMID:40640702

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12247349/

Abstract

BACKGROUND

The APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor family plays a crucial role in plant development and stress responses. Characterized by the conserved AP2 DNA-binding domain, this family includes key subfamilies such as ERF, AP2, and RAV. Understanding the composition and evolutionary dynamics of the family in coffee is essential for advancing the development of stress-resilient cultivars. Leveraging recent genomic resources for (robusta coffee), , and , this study aims to provide a comprehensive genome-wide characterization and evolutionary analysis of the family within these economically important species.

RESULTS

A total of 453 genes were identified across the three species, constituting approximately 0.48% of their protein-coding genes. Chromosomal mapping and synteny analysis revealed a high degree of conservation among , , and , reflecting their close evolutionary relationships. Gene duplication events were found to significantly contribute to the expansion of the family, accounting for 16% of the total gene count. Subgroup IX, associated with disease resistance, exhibited substantial variation between the two parental species and their descendant subgenomes in , indicating possible lineage-specific gene loss or expansion. Similarly, Subgroup III, linked to temperature tolerance, showed distinct expansion patterns among the coffee species, hinting at adaptive responses to varied environments.

CONCLUSIONS

These comparative analyses of the transcription factor family in species provide valuable insights into the adaptive evolution of this gene family under diverse environmental stresses. The observed subgroup-specific variations provide a basis for further functional studies and underscore potential candidates for breeding programs aimed at enhancing stress resilience and sustainability in coffee production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12864-025-11850-0.

摘要

背景

APETALA2/乙烯响应因子（AP2/ERF）转录因子家族在植物发育和胁迫响应中起着至关重要的作用。该家族以保守的AP2 DNA结合结构域为特征，包括ERF、AP2和RAV等关键亚家族。了解咖啡中该家族的组成和进化动态对于推进抗逆品种的开发至关重要。利用最近的基因组资源（罗布斯塔咖啡）、[未提及具体物种2]和[未提及具体物种3]，本研究旨在对这些经济重要物种中的AP2/ERF家族进行全面的全基因组表征和进化分析。

结果

在这三个咖啡物种中总共鉴定出453个AP2/ERF基因，约占其蛋白质编码基因的0.48%。染色体定位和共线性分析表明，[未提及具体物种1]、[未提及具体物种2]和[未提及具体物种3]之间具有高度的保守性，反映了它们密切的进化关系。发现基因复制事件对AP2/ERF家族的扩展有显著贡献，占基因总数的16%。与抗病性相关的第九亚组在[未提及具体物种1]的两个亲本物种及其后代亚基因组之间表现出显著差异，表明可能存在谱系特异性的基因丢失或扩展。同样，与耐温性相关的第三亚组在咖啡物种中表现出不同的扩展模式，暗示了对不同环境的适应性反应。