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AP2/ERF 基因的比较和表达分析揭示了茄科中 ERF 基因的拷贝数扩张和潜在功能。

Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae.

机构信息

Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.

出版信息

BMC Plant Biol. 2023 Jan 23;23(1):48. doi: 10.1186/s12870-022-04017-6.

DOI:10.1186/s12870-022-04017-6
PMID:36683040
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9869560/
Abstract

BACKGROUND

The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking.

RESULTS

Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups.

CONCLUSIONS

Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.

摘要

背景

AP2/ERF 基因家族是一类重要的转录因子超家族，在植物应对非生物胁迫和发育中发挥着重要作用。然而，茄科植物 AP2/ERF 基因的综合研究还很缺乏。

结果

本研究更新了 8 种茄科植物（包括拟南芥和水稻）基因组中 AP2/ERF 基因的注释，共鉴定出 2195 个 AP2/ERF 基因，其中 368 个（17%）为新鉴定的基因。基于系统发育分析，我们观察到这些基因的拷贝数发生了扩张，特别是茄科特有的乙烯响应因子（ERF）亚家族的基因。从染色体定位和共线性分析的结果来看，我们发现辣椒、番茄和马铃薯属于 ERF 亚家族的 AP2/ERF 基因形成串联排列，并且大多数是种特异性的，在其他物种中没有同源基因，这导致了茄科 AP2/ERF 基因库的分化。我们推测这些基因主要是在这些物种分化后通过近期基因复制产生的。转录组分析表明，这些基因在辣椒和番茄对非生物胁迫的反应中具有潜在的功能，特别是在 ERF 亚家族中。

结论

本研究结果为 AP2/ERF 基因提供了全面的信息，并深入了解了这些基因在茄科植物中的结构、进化和功能作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/6802e4af8ba6/12870_2022_4017_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/ee7f8771540c/12870_2022_4017_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/9f12549e3b61/12870_2022_4017_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/4b65272d2b40/12870_2022_4017_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/7a7f02602bb6/12870_2022_4017_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/6802e4af8ba6/12870_2022_4017_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/ee7f8771540c/12870_2022_4017_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/9f12549e3b61/12870_2022_4017_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/4b65272d2b40/12870_2022_4017_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/7a7f02602bb6/12870_2022_4017_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7caf/9869560/6802e4af8ba6/12870_2022_4017_Fig5_HTML.jpg

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