Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants
Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants
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蔷薇科植物MLO基因家族的全基因组鉴定及进化分析
DOI：
10.1016/j.hpj.2020.07.007
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发表时间：
2021-08
影响因子：
5.7
通讯作者：
Qiu Xianqin
中科院分区：
文献类型：
--
作者：
Tian Yongxian;Wang Qigang;Zhang Hao;Zhou Ningning;Yan Huijun;Jian Hongying;Li Shubin;Xiang Guisheng;Tang Kaixue;Qiu Xianqin
缺乏野生型MLO蛋白的突变体对白粉菌表现出广谱抗性，细胞死亡控制失调，细胞对发育或非生物刺激有自发死亡反应。为了了解蔷薇科植物MLO基因家族的进化和分化模式，我们基于生物信息学的方法，系统地分析了绒毛李、桃、梅、苹果、梨和西红莓的全基因组数据。利用邻接法、最大似然法和贝叶斯法三种系统发育方法，从6种蔷薇科植物中鉴定出117个MLO基因。3种系统发育分析方法的结果均支持将这些基因分为6个分支。保守基序分析发现，所有MLO蛋白中仅存在基序2，且含有3个几乎不变的氨基酸残基。这些结果表明，Motif 2可能与MLO基因家族所共有。这些基因的结构特征在不同物种的序列长度上表现出很大的差异，尽管外显子的长度和数量表现出高度的相似性。选择压力分析显示6个支系间存在极显著差异，其中2个、1个和1个位点(S)分别在III、IV和VI支系中检测到显著正选择。这些正向选择位点是促进MLO基因功能分化的重要动力。功能差异分析表明，差异显著的部位位于MLO基因的结构域内。功能距离分析表明，V分支在进化过程中具有更多的保守功能，可能保留了更多的原有功能。然而，作为一个专门的功能角色，分支I可能经历了广泛的功能限制。此外，玫瑰科植物MLO基因最原始的功能可能与其对白粉病抗性的进化有关，而白粉病抗性由于基因复制后的不同进化速率而逐渐进化为调控花发育、控制根系形态和种子进化等功能。这些结果为进一步研究植物MLO基因家族的分子进化模式提供了理论依据。
Mutants lacking wild-type MLO (Mildew resistance Locus O) proteins show broad-spectrum resistance to the powdery mildew fungus, and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli. In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants, we analysed systematically genome-wide data from Fragaria vesca, Prunus persica, Prunus mume, Malus domestica, Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods. Using three phylogenetic methods (the neighbour-joining, maximum likelihood, and Bayesian methods), we identified 117 MLO genes from 6 Rosaceae species. The results of all three phylogenetic analysis methods supported that these genes were divided into six clades. Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues. The findings indicated that motif 2 might be shared by the MLO gene family. The structural features of these genes showed large variations in sequence length among different species, although the lengths and the numbers of exons exhibited high degrees of similarity. Selective pressure analysis showed extremely significant differences in all 6 clades,with 2, 1, and 1 site(s) under significant positive selection detected in clades III, IV, and VI, respectively. These positive selection siteswere important driving forces for the promotion of the functional differentiation of the MLO genes. Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes. Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process. However, clade I may have undergone extensive altered functional constraints as a specialised functional role. Moreover, the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew, which then gradually evolved into functions such as the regulation of flower development, the control of root morphology, and seed evolution due to the different evolutionary rates after gene duplication. These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.
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DOI：
10.1007/s11032-009-9323-6
发表时间：
2010-01
期刊：
Molecular breeding : new strategies in plant improvement
影响因子：
--
作者：
Pavan S;Jacobsen E;Visser RG;Bai Y
通讯作者：
Bai Y
影响因子：
4.8
作者：
Kim, MC;Lee, SH;Cho, MJ
通讯作者：
Cho, MJ
影响因子：
5.3
作者：
Almeida NF;Leitão ST;Krezdorn N;Rotter B;Winter P;Rubiales D;Vaz Patto MC
通讯作者：
Vaz Patto MC
影响因子：
4.6
作者：
Rispail N;Rubiales D
通讯作者：
Rubiales D
DOI：
10.1093/bioinformatics/btw108
发表时间：
2016-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Katoh K;Standley DM
通讯作者：
Standley DM