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    杨锐霞, 尹鹏, 刘晓, 王艳, 刘家福, 徐吉臣. 旱柳扩展蛋白基因家族与基因组分化[J]. 北京林业大学学报, 2021, 43(1): 37-48. DOI: 10.12171/j.1000-1522.20200216
    引用本文: 杨锐霞, 尹鹏, 刘晓, 王艳, 刘家福, 徐吉臣. 旱柳扩展蛋白基因家族与基因组分化[J]. 北京林业大学学报, 2021, 43(1): 37-48. DOI: 10.12171/j.1000-1522.20200216
    shu
    Yang Ruixia, Yin Peng, Liu Xiao, Wang Yan, Liu Jiafu, Xu Jichen. Expansin gene family in association with the genome differentiation of Salix matsudana[J]. Journal of Beijing Forestry University, 2021, 43(1): 37-48. DOI: 10.12171/j.1000-1522.20200216
    Citation: Yang Ruixia, Yin Peng, Liu Xiao, Wang Yan, Liu Jiafu, Xu Jichen. Expansin gene family in association with the genome differentiation of Salix matsudana[J]. Journal of Beijing Forestry University, 2021, 43(1): 37-48. DOI: 10.12171/j.1000-1522.20200216
    shu

    旱柳扩展蛋白基因家族与基因组分化

    Expansin gene family in association with the genome differentiation of Salix matsudana

      摘要
    • 摘要:
        目的  扩展蛋白是植物中重要的基因家族之一，在生长发育和逆境抗性过程中发挥重要的作用。本研究拟探讨旱柳中的扩展蛋白基因组成变化，为理解旱柳AA、BB基因组的分化提供理论依据，也为柳树分子设计育种提供参考。
        方法  本研究基于毛果杨扩展蛋白基因氨基酸序列，鉴定旱柳中的扩展蛋白基因；通过生物信息学软件，分析旱柳AA、BB基因组扩展蛋白基因家族的特征和变化。
        结果  在异源四倍体旱柳基因组中鉴定了65个扩展蛋白基因，其中AA基因组32个、BB基因组33个，共有的扩展蛋白基因28个，有3个基因产生了重复；AA、BB基因组中各有3个扩展蛋白基因缺失，并分别有2个和1个基因结构域发生了缺失。基因结构分析表明，部分AA、BB基因组的对应基因在内含子数量和内含子剪切位点等方面存在明显变化。在密码子使用选择上，AA、BB基因组间各含有5个高频密码子，分别含有5个和10个最优密码子，部分密码子如AGG和UAG等的使用频率有很大的差别。比较蛋白理化性质，AA、BB基因组的扩展蛋白在亲疏水性、结构稳定性方面存在不同程度的变化。进化分析显示，两套基因组中EXPA23基因经历了正选择，其他同源基因经历了纯化选择，但Ka/Ks值变化较大。
        结论  旱柳AA、BB基因组扩展蛋白家族具有各自的组成、结构及表达特征，是基因组分化的基础，体现了扩展蛋白在物种分化和分类中的重要地位。

       

      Abstract:
        Objective  Expansin, an important gene family in plants, plays a critical role in plant growth and development and resistance to various biotic and abiotic stresses. The purpose of this study was to investigate the variation of expansin genes in Salix matsudana so as to provide theoretical basis for understanding the AA and BB genome differentiation in Salix matsudana, and to contribute greatly for molecular design and breeding of Salix.
        Method  According to the expansin gene sequences of Populus trichocarpa, the expansin family genes in Salix matsudana were individually identified. The characteristics and variations of the expansin genes in AA and BB genome were analyzed and evaluated by the bioinformatics softwares.
        Result  A total of 65 expansin genes were identified in allotetraploid Salix matsudana based on the conservation of sequence and structure of the expansin genes. Both genomes shared 28 genes with 3 genes duplicated. Moreover, 3 expansin genes were missed and 2 genes were with a domain deficient in AA genome, while 3 expansin genes were missed and 1 gene was with a domain deficient in BB genome, respectively. Gene structure analysis showed the considerable changes in the number and cutting sites of intron between the relative gene pairs of both genomes. Besides, AA and BB expansin genes both had 5 high-frequency codons, and separately had 5 and 10 optimal codons. Some codons had significant usage bias such as AGG and UAG. Evaluation of the protein physicochemical properties showed that the AA and BB expansins changed a lot, especially in terms of hydrophilicity and structural stability. Ka/Ks calculation displayed that EXPA23 gene had experienced positive selection during AA and BB genome differentiation, while the other genes underwent purification selection with Ka/Ks value changed widely.
        Conclusion  The report here characterized the composition, structure and expression of the expansin genes in AA and BB genomes, which probably advanced the genome differentiation and further confirmed the important status of expansins in species classification.

       

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