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首页> 外文期刊>International journal of plant sciences >BIOINFORMATIC IDENTIFICATION AND ANALYSIS OF CELL WALL EXTENSINS IN THREE ARABIDOPSIS SPECIES
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BIOINFORMATIC IDENTIFICATION AND ANALYSIS OF CELL WALL EXTENSINS IN THREE ARABIDOPSIS SPECIES

机译：三种拟南芥种细胞壁扩展素的生物信息学鉴定和分析

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Premise of research. Extensins (EXTs) are members of the cell wall hydroxyproline-rich glycoprotein superfamily and play important roles in plant growth, development, and defense. Bioinformatic analysis has identified EXTs for a number of plant species, including the model plant Arabidopsis thaliana, but none of these studies examined plants from the same genus. Methodology. Here we report on the bioinformatic identification and analysis of EXTs in Arabidopsis lyrata and Arabidopsis halleri, two of the closest relatives of A. thaliana, based on amino acid motif searches using the BIO OHIO 2.0 program. Phylogenetic trees for the various EXT subclasses were constructed using both maximum likelihood and maximum parsimony methods. Homologous proteins were revealed using the OrthoMCL program. Pivotal results. The total numbers and subclasses of EXTs were similar in all three species. In A. lyrata, 61 EXTs were identified, including 15 classical EXTs, 10 short EXTs, eight leucine-rich repeat EXTs (LRXs), 14 proline-rich EXT-like receptor kinases (PERKs), five formin homology EXTs (FHXs), four hybrid hydroxyproline-rich glycoproteins (HRGPs), and five other chimeric EXTs. In A. halleri, 65 EXTs were identified, including 13 classical EXTs, 14 short EXTs, eight LRXs, 14 PERKs, six FHXs, four hybrid HRGPs, and six other chimeric EXTs. For comparison, 69 EXTs were identified in A. thaliana, including 19 classical EXTs, 13 short EXTs, 11 LRXs, 12 PERKs, six FHXs, four hybrid HRGPs, and four other chimeric EXTs. Phylogenetic trees and cluster analysis revealed a number of potential orthologous and paralogous proteins among the three species. Conclusions. The identified EXTs and their homologous proteins among A. lyrata, A. halleri, and A. thaliana provide insight into the evolution and functions of EXTs in related species within the same genus. This project offers an excellent example of studying a model system consisting of three closely related species, in which diverse genetic resources and biological data make it possible to address fundamental evolutionary questions that cannot be addressed in a single species.
机译：研究前提。延伸蛋白（EXTs）是富含细胞壁羟脯氨酸的糖蛋白超家族的成员，在植物生长，发育和防御中起重要作用。生物信息学分析已经确定了许多植物物种的EXTs，包括模式植物拟南芥，但是这些研究都没有检查相同属的植物。方法。在这里，我们基于使用BIO OHIO 2.0程序进行的氨基酸基序搜索，报告了拟南芥的两个近亲中拟南芥和拟南芥中EXTs的生物信息学鉴定和分析。使用最大似然和最大简约方法构建了各种EXT子类的系统发育树。使用OrthoMCL程序揭示同源蛋白质。关键的结果。在所有三个物种中，EXTs的总数和子类相似。在拟南芥中鉴定出61个EXT，包括15个经典EXT，10个短EXT，8个富含亮氨酸的重复EXT（LRXs），14个富含脯氨酸的EXT-like受体激酶（PERK），5个FORMIN同源性EXT（FHX），四个杂合富含羟脯氨酸的糖蛋白（HRGP）和其他五个嵌合EXT。在A. halleri中，鉴定出65个EXT，包括13个经典EXT，14个短EXT，8个LRX，14个PERK，6个FHX，4个混合HRGP和6个其他嵌合EXT。为了进行比较，在拟南芥中鉴定出69个EXT，包括19个经典EXT，13个短EXT，11个LRX，12个PERK，6个FHX，4个混合HRGP和4个其他嵌合EXT。系统发育树和聚类分析揭示了这三个物种中许多潜在的直系同源和旁系同源蛋白。结论。经鉴定的EXTs及其在A. lyrata，A。halleri和A. thaliana中的同源蛋白可洞察同一属内相关物种中EXTs的进化和功能。该项目为研究由三个密切相关的物种组成的模型系统提供了一个极好的示例，在该模型系统中，多样化的遗传资源和生物学数据使得有可能解决单个物种无法解决的基本进化问题。

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