基因表达和调控网络为固氮和丛枝菌根共生的相似性提供了新的见解。

IF 4 2区 生物学 Q2 CELL BIOLOGY
Zefeng Wu, Yali Sun, Jun Yang, Zigang Liu, Yining Niu, Xiaowei Zhang
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引用次数: 0

摘要

虽然发生在植物和根瘤菌之间的进化较年轻的固氮共生(NFS)主要局限于豆科植物物种,但它们表现出一系列与更古老的丛枝菌根共生(AMS)共同的高度保守特征。越来越多的共生调节基因已经通过遗传分析或系统基因组分析进行了表征。然而,AMS和NFS的转录调控机制的潜在相似性和特异性在很大程度上仍不清楚。本研究系统分析了三种豆科植物(Medicago truncatula, Glycine max和Lotus japonicus)在AMS和NFS过程中的基因表达变化。此外,我们还研究了3种非豆科植物——番茄茄(Solanum lycopersicum)、玉米(Zea mays)和水稻(Oryza sativa)在AMS过程中的基因表达变化。我们在各自的寄主植物中鉴定了数千个被AMS或NFS激活的基因。通过比较基因组学分析,我们系统地探索了AMS或NFS应答基因的保守性和特异性。以M. truncatula和G. max为例,我们利用XGboost机器学习模型在这两个物种中构建了基于共表达的AMS和NFS基因调控网络。通过这种方法,我们成功地阐明了两种共生类型在基因调控网络水平上的相似性和独特性。此外,利用已知的共生基因作为查询,我们确定了许多与AMS和NFS密切相关的基因。总体而言,通过深入的基因表达谱分析和调控网络分析,我们的研究结果表明,尽管豆科植物的NFS具有与AMS相似的调控回路,但存在一定的共生类型特异性分子成分。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.

Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks (GRNs) for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the GRN level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.

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来源期刊
Plant and Cell Physiology
Plant and Cell Physiology 生物-细胞生物学
CiteScore
8.40
自引率
4.10%
发文量
166
审稿时长
1.7 months
期刊介绍: Plant & Cell Physiology (PCP) was established in 1959 and is the official journal of the Japanese Society of Plant Physiologists (JSPP). The title reflects the journal''s original interest and scope to encompass research not just at the whole-organism level but also at the cellular and subcellular levels. Amongst the broad range of topics covered by this international journal, readers will find the very best original research on plant physiology, biochemistry, cell biology, molecular genetics, epigenetics, biotechnology, bioinformatics and –omics; as well as how plants respond to and interact with their environment (abiotic and biotic factors), and the biology of photosynthetic microorganisms.
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