利用系统发育图谱分析 365 个植物物种的共同进化信号,挖掘互花叶斯巴达盐胁迫相关基因

IF 4.6 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Shang Gao, Shoukun Chen, Maogeng Yang, Jinran Wu, Shihua Chen, Huihui Li
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引用次数: 0

摘要

随着测序物种数量的不断增加,系统发育剖析(PP)已成为一种基于共同进化信息预测功能基因的强大方法。然而,它在植物基因组学中的潜力尚未得到充分挖掘。在此背景下,我们结合了机器学习和PP的力量,利用从365种植物中获得的进化信息,鉴定了盐生禾本科植物Spartina alterniflora中与盐胁迫相关的基因。结果表明,与已知盐胁迫相关基因高度共同进化的基因富集于离子转运、解毒和代谢途径等生物过程中。在离子转运方面,5个已发现的编码2个钠转运体和3个钾转运体的基因被证实能够吸收Na+。此外,我们还发现了与毛状体相关的 AtR3-MYB 基因的两个直向同源基因 SaCPC1 和 SaCPC2,它们可能参与盐度反应。与 SaCPCs 共同进化的基因富含与昼夜节律和非生物胁迫响应相关的功能。总之,这项工作证明了利用进化信息挖掘盐胁迫相关基因的可行性,凸显了PP作为植物功能基因组学宝贵工具的潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Mining salt stress-related genes in Spartina alterniflora via analyzing co-evolution signal across 365 plant species using phylogenetic profiling

With the increasing number of sequenced species, phylogenetic profiling (PP) has become a powerful method to predict functional genes based on co-evolutionary information. However, its potential in plant genomics has not yet been fully explored. In this context, we combined the power of machine learning and PP to identify salt stress-related genes in a halophytic grass, Spartina alterniflora, using evolutionary information generated from 365 plant species. Our results showed that the genes highly co-evolved with known salt stress-related genes are enriched in biological processes of ion transport, detoxification and metabolic pathways. For ion transport, five identified genes coding two sodium and three potassium transporters were validated to be able to uptake Na+. In addition, we identified two orthologs of trichome-related AtR3-MYB genes, SaCPC1 and SaCPC2, which may be involved in salinity responses. Genes co-evolved with SaCPCs were enriched in functions related to the circadian rhythm and abiotic stress responses. Overall, this work demonstrates the feasibility of mining salt stress-related genes using evolutionary information, highlighting the potential of PP as a valuable tool for plant functional genomics.

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CiteScore
7.70
自引率
2.80%
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