College of Forestry, Shenyang Agricultural University, Shenyang, China.
Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China.
BMC Genomics. 2023 Jun 27;24(1):358. doi: 10.1186/s12864-023-09469-0.
WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKY genes (PsWRKY) remains lacking.
This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions.
Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.
WRKY 转录因子是植物中一个重要的基因家族，在发育、代谢、防御、分化和应激反应等各种生物学过程中发挥着关键作用。尽管 WRKY 基因家族在许多植物物种中得到了广泛的研究和分析，但对西伯利亚李属（Prunus sibirica）的 WRKY 基因（PsWRKY）的研究仍然缺乏。
本研究基于西伯利亚李属的全基因组数据，采用生物信息学方法分析了 PsWRKY 基因家族成员的基本理化性质、系统发育、基因结构、顺式作用元件和基因本体（GO）注释。共鉴定出 55 个 WRKY 基因，不均匀分布在 8 条染色体上。基于系统发育分析，这些 WRKY 基因被分为三个主要组：I 组、II 组（II-a、II-b、II-c、II-d、II-e）和 III 组。不同亚家族的成员具有不同的顺式作用元件、保守基序和内含子-外显子结构，表明 WRKY 家族的功能异质性。亚细胞定位预测表明，PsWRKY 主要位于细胞核内。鉴定出 20 对复制基因，片段复制事件可能在 PsWRKY 基因家族扩张中发挥重要作用。Ka/Ks 比值分析表明，PsWRKY 家族的同源基因主要通过选择进行纯化。此外，GO 注释分析表明，WRKY 基因家族主要参与对外界刺激、免疫系统过程和生殖过程的响应。此外，定量实时 PCR（qRT-PCR）分析表明，23 个 PsWRKY 在一个或多个组织（雌蕊和根）中高度表达，并且 PsWRKY 在不同低温胁迫条件下表现出特定的表达模式。
我们的研究结果为进一步探索和验证西伯利亚李属中的 WRKY 提供了科学依据。
