Genome-wide identification and analysis of Snf2 gene family in U’s triangle model reveals changes in Snf2 during polyploidization

【作者】 钱方； Yujun Xue； Wenjie Guan； Guangqin Cai； 伍晓明；

【Author】 Fang Qian;Yujun Xue;Wenjie Guan;Guangqin Cai;Xiaoming Wu;Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences;

【机构】 Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences；

【摘要】 【Background】Sucrose nonfermenting 2(Snf2) family 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. The six major Brassica species in U’s triangle model are widely cultivated crops for oilseed and vegetables, which is an ideal model for the analysis of allopolyploid evolution. However, the comparative analysis of Snf2 gene family in U’s triangle model has remained rare until now.【Method】Bioinformatic methods were used to identify the Snf2 gene family in the U’s triangle model. These genes were comprehensively analysed by phylogeny, physicochemical properties, conserved sequences, gene duplication, evolution, promoter sequences, and Gene Ontology(GO) functional, expression profile, quantitative real-time PCR(qRT-PCR), etc.【Results】Here, 405 Snf2 genes were identified in U’s triangle model, comprising 53, 50, and 46 in the diploid progenitors Brassica rapa, Brassica nigra, and Brassica oleracea and 93, 91, and 72 in the allotetraploid Brassica juncea, Brassica napus, and Brassica carinata, respectively. These Snf2 genes were classified into six clades, which were further subdivided into 18 subfamilies, and each subclade contained the similar conserved motifs and domains. The results of chromosomal distributions and gene structures showed that the majority of Snf2 genes were highly conserved among the six species, indicating that less dynamic changes occurred during genome evolution and polyploidization. Analysis of duplication events suggested that the duplication modes of U’s triangle model were diverse and the expansion of most Snf2 in Brassica occurred primarily through dispersed duplication(DSD) events. Additionally, Ka/Ks analysis suggested that most of the Snf2 genes were under purifying selection in the process of evolution. Cis-acting element and GO analysis revealed that most of the Snf2 genes were associated with various environmental stress. Furthermore, the expression pattern clarified the transcriptional levels of BnaSnf2(Snf2 gene in B. napus) genes in various tissues and under salt stress in B. napus. The results were verified by qRT-PCR analysis and suggest that Snf2 genes significantly contribute to salt stress tolerance in Brassica species. 【 Conclusion 】 The aforementioned results provide a comprehensive understanding of the Snf2 genes in U’s triangle model which will facilitate further function analysis of the Snf2 genes in Brassica plants.更多还原

【Abstract】 【Background】Sucrose nonfermenting 2(Snf2) family 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. The six major Brassica species in U’s triangle model are widely cultivated crops for oilseed and vegetables, which is an ideal model for the analysis of allopolyploid evolution. However, the comparative analysis of Snf2 gene family in U’s triangle model has remained rare until now.【Method】Bioinformatic methods were used to identify the Snf2 gene family in the U’s triangle model. These genes were comprehensively analysed by phylogeny, physicochemical properties, conserved sequences, gene duplication, evolution, promoter sequences, and Gene Ontology(GO) functional, expression profile, quantitative real-time PCR(qRT-PCR), etc.【Results】Here, 405 Snf2 genes were identified in U’s triangle model, comprising 53, 50, and 46 in the diploid progenitors Brassica rapa, Brassica nigra, and Brassica oleracea and 93, 91, and 72 in the allotetraploid Brassica juncea, Brassica napus, and Brassica carinata, respectively. These Snf2 genes were classified into six clades, which were further subdivided into 18 subfamilies, and each subclade contained the similar conserved motifs and domains. The results of chromosomal distributions and gene structures showed that the majority of Snf2 genes were highly conserved among the six species, indicating that less dynamic changes occurred during genome evolution and polyploidization. Analysis of duplication events suggested that the duplication modes of U’s triangle model were diverse and the expansion of most Snf2 in Brassica occurred primarily through dispersed duplication(DSD) events. Additionally, Ka/Ks analysis suggested that most of the Snf2 genes were under purifying selection in the process of evolution. Cis-acting element and GO analysis revealed that most of the Snf2 genes were associated with various environmental stress. Furthermore, the expression pattern clarified the transcriptional levels of BnaSnf2(Snf2 gene in B. napus) genes in various tissues and under salt stress in B. napus. The results were verified by qRT-PCR analysis and suggest that Snf2 genes significantly contribute to salt stress tolerance in Brassica species. 【 Conclusion 】 The aforementioned results provide a comprehensive understanding of the Snf2 genes in U’s triangle model which will facilitate further function analysis of the Snf2 genes in Brassica plants.更多还原