Comprehensive genome-wide identification of Snf2 gene family and their expression profile under salt stress in six Brassica species of U's triangle model.

IF 3.6 3区 生物学 Q1 PLANT SCIENCES Planta Pub Date : 2024-07-10 DOI:10.1007/s00425-024-04473-4
Fang Qian, Dan Zuo, Yujun Xue, Wenjie Guan, Naseeb Ullah, Jiarong Zhu, Guangqin Cai, Bin Zhu, Xiaoming Wu
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Abstract

Main conclusion: We comprehensively identified and analyzed the Snf2 gene family. Some Snf2 genes were involved in responding to salt stress based on the RNA-seq and qRT-PCR analysis. Sucrose nonfermenting 2 (Snf2) proteins are core components of chromatin remodeling complexes that not only alter DNA accessibility using the energy of ATP hydrolysis, but also play a critical regulatory role in growth, development, and stress response in eukaryotes. However, the comparative study of Snf2 gene family in the six Brassica species in U's triangle model remains unclear. Here, a total of 405 Snf2 genes were identified, comprising 53, 50, and 46 in the diploid progenitors: Brassica rapa (AA, 2n = 20), Brassica nigra (BB, 2n = 16), and Brassica oleracea (CC, 2n = 18), and 93, 91, and 72 in the allotetraploid: Brassica juncea (AABB, 2n = 36), Brassica napus (AACC, 2n = 38), and Brassica carinata (BBCC, 2n = 34), respectively. These genes were classified into six clades and further divided into 18 subfamilies based on their conserved motifs and domains. Intriguingly, these genes showed highly conserved chromosomal distributions and gene structures, indicating that few dynamic changes occurred during the polyploidization. The duplication modes of the six Brassica species were diverse, and the expansion of most Snf2 in Brassica occurred primarily through dispersed duplication (DSD) events. Additionally, the majority of Snf2 genes were under purifying selection during polyploidization, and some Snf2 genes were associated with various abiotic stresses. Both RNA-seq and qRT-PCR analysis showed that the expression of BnaSnf2 genes was significantly induced under salt stress, implying their involvement in salt tolerance response in Brassica species. The results provide a comprehensive understanding of the Snf2 genes in U's triangle model species, which will facilitate further functional analysis of the Snf2 genes in Brassica plants.

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全基因组范围内全面鉴定 U's triangle 模型中 6 种芸薹属植物的 Snf2 基因家族及其在盐胁迫下的表达谱。
主要结论我们对Snf2基因家族进行了全面鉴定和分析。根据 RNA-seq 和 qRT-PCR 分析,一些 Snf2 基因参与了对盐胁迫的响应。蔗糖不发酵2(Snf2)蛋白是染色质重塑复合物的核心成分,它不仅利用ATP水解的能量改变DNA的可及性,而且在真核生物的生长、发育和应激反应中起着重要的调控作用。然而,乌氏三角模型中六种芸薹属植物 Snf2 基因家族的比较研究仍不清楚。本文共鉴定出 405 个 Snf2 基因,其中二倍体原基中分别有 53 个、50 个和 46 个:芸苔属(AA,2n = 20)、黑芸苔属(BB,2n = 16)和油甘蓝属(CC,2n = 18)的二倍体中分别有 53、50 和 46 个 Snf2 基因,异源四倍体中分别有 93、91 和 72 个 Snf2 基因:芸苔属(AABB,2n = 36)、油菜属(AACC,2n = 38)和甘蓝属(BBCC,2n = 34)分别有 93、91 和 72 个基因。这些基因被分为 6 个支系,并根据其保守基序和结构域进一步分为 18 个亚科。耐人寻味的是,这些基因的染色体分布和基因结构高度保守,表明在多倍体化过程中几乎没有发生动态变化。六个芸苔属物种的复制模式多种多样,大多数 Snf2 在芸苔属中的扩展主要是通过分散复制(DSD)事件实现的。此外,大多数Snf2基因在多倍体化过程中受到纯化选择,一些Snf2基因与各种非生物胁迫有关。RNA-seq和qRT-PCR分析表明,BnaSnf2基因的表达在盐胁迫下被显著诱导,这意味着它们参与了芸苔属植物的耐盐反应。这些研究结果为全面了解乌江三角洲模式物种中的Snf2基因提供了依据,有助于进一步对芸薹属植物中的Snf2基因进行功能分析。
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来源期刊
Planta
Planta 生物-植物科学
CiteScore
7.20
自引率
2.30%
发文量
217
审稿时长
2.3 months
期刊介绍: Planta publishes timely and substantial articles on all aspects of plant biology. We welcome original research papers on any plant species. Areas of interest include biochemistry, bioenergy, biotechnology, cell biology, development, ecological and environmental physiology, growth, metabolism, morphogenesis, molecular biology, new methods, physiology, plant-microbe interactions, structural biology, and systems biology.
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