Multi-omics analyses reveal new insights into nutritional quality changes of alfalfa leaves during the flowering period

Liu, Yinghao; Fan, Wenqiang; Cheng, Qi; Zhang, Lianyi; Cai, Ting; Shi, Quan; Zuo, Wangmeng; Chang, Chun; Yin, Qiang; Jiang, Xiaowei; Jin, Ke

doi:10.3389/fpls.2022.995031

Cited by 6 publications

(3 citation statements)

References 56 publications

(53 reference statements)

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“…Flavonoids are secondary metabolites widely distributed in plants. As a flavonoid 3 'hydroxylase, CYP75B1 belongs to the cytochrome P450 monooxygenase family, and it participates in the flavonoid metabolic pathway [32]. More importantly, the expression of CYP75B1 can induce flavonoid biosynthesis to regulate the ROS homeostasis [33].…”

Section: Identification Of Degs and Function Analysis In Plantmentioning

confidence: 99%

Dual RNA-Seq Analysis Pinpoints to a BalancedRegulation between Symbiosis and Immunity in the Medicago truncatula-Sinorhizobium meliloti Symbiotic Interactions

Zhang,

Wu,

Zhao

et al. 2023

Preprint

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Legume-rhizobial symbiosis leads to to the formation of root nodules, where rhizobia reside and develop into bacteroids to reduce nitrogen into ammonium for plant growth, which leaves an opening question as how plant immunity is attenuated in nodules in the presence of large number of foreign bacteria. In Medicago truncatula, mutation in NAD1 (Nodules with Activated Defense 1) only produces necrotic nodules with overactivated immunity, indicating NAD1 is an indispensable component required for suppressing immunity in nodules. In this study, a dual RNA-seq transcriptomic technology was performed to extensively analyze gene expressions in nad1-1 mutant nodules. We indenifited 89 DEGs in symbiotic nitrogen fixation and 89 DEGs in immunity in Medicago truncatula at 10 dpi. Simultaneously, we indenifited 27 DEGs in fix and nif genes in Sinorhizobium meliloti. Then we identified 56 DEGs related to stress, including ROS, NO, and NCR, most of which were upregulated in Sinorhizobium meliloti. Our analyses of nitrogen fixation-defective plant nad1-1 mutants with overactivated defense indicate that host use plant immunity to control massive bacterial colonization during early and late symbiotic stages. Our findings provide insight into the function of NAD1 in improvement or inhibition of plant immune response to maintain symbiosis during rhizobial endosymbiosis.

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Section: Identification Of Degs and Function Analysis In Plantmentioning

confidence: 99%

Dual RNA-Seq Analysis Pinpoints to a BalancedRegulation between Symbiosis and Immunity in the Medicago truncatula-Sinorhizobium meliloti Symbiotic Interactions

Zhang,

Wu,

Zhao

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Flavonoids are secondary metabolites widely distributed in plants. As a flavonoid 3 -hydroxylase, CYP75B1 belongs to the cytochrome P450 monooxygenase family, and it participates in the flavonoid metabolic pathway [45]. More importantly, the expression of CYP75B1 can induce flavonoid biosynthesis to regulate the ROS homeostasis [46].…”

Section: Identification Of Degs From Hosts In the M Truncatula Nad1 N...mentioning

confidence: 99%

“…ticipates in the flavonoid metabolic pathway [45]. More importantly, the expression of CYP75B1 can induce flavonoid biosynthesis to regulate the ROS homeostasis [46].…”

Section: Identification Of Degs From Symbionts In the M Truncatula Na...mentioning

confidence: 99%

Dual RNA-Seq Analysis Pinpoints a Balanced Regulation between Symbiosis and Immunity in Medicago truncatula-Sinorhizobium meliloti Symbiotic Nodules

Zhang,

Wu,

Zhao

et al. 2023

IJMS

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Legume–rhizobial symbiosis initiates the formation of root nodules, within which rhizobia reside and differentiate into bacteroids to convert nitrogen into ammonium, facilitating plant growth. This process raises a fundamental question: how is plant immunity modulated within nodules when exposed to a substantial number of foreign bacteria? In Medicago truncatula, a mutation in the NAD1 (Nodules with Activated Defense 1) gene exclusively results in the formation of necrotic nodules combined with activated immunity, underscoring the critical role of NAD1 in suppressing immunity within nodules. In this study, we employed a dual RNA-seq transcriptomic technology to comprehensively analyze gene expression from both hosts and symbionts in the nad1-1 mutant nodules at different developmental stages (6 dpi and 10 dpi). We identified 89 differentially expressed genes (DEGs) related to symbiotic nitrogen fixation and 89 DEGs from M. truncatula associated with immunity in the nad1-1 nodules. Concurrently, we identified 27 rhizobial DEGs in the fix and nif genes of Sinorhizobium meliloti. Furthermore, we identified 56 DEGs from S. meliloti that are related to stress responses to ROS and NO. Our analyses of nitrogen fixation-defective plant nad1-1 mutants with overactivated defenses suggest that the host employs plant immunity to regulate the substantial bacterial colonization in nodules. These findings shed light on the role of NAD1 in inhibiting the plant’s immune response to maintain numerous rhizobial endosymbiosis in nodules.

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Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

Bejerman,

Dietzgen,

Debat

2023

Preprint

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Cytorhabdoviruses (genusCytorhabdovirus, familyRhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genusCytorhabdovirushave unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented cytorhabdoviruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the familyRhabdoviridae. Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (familyFimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genusCytorhabdovirusinto three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus, but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.

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Multi-omics analyses reveal new insights into nutritional quality changes of alfalfa leaves during the flowering period

Cited by 6 publications

References 56 publications

Dual RNA-Seq Analysis Pinpoints to a BalancedRegulation between Symbiosis and Immunity in the Medicago truncatula-Sinorhizobium meliloti Symbiotic Interactions

Dual RNA-Seq Analysis Pinpoints to a BalancedRegulation between Symbiosis and Immunity in the Medicago truncatula-Sinorhizobium meliloti Symbiotic Interactions

Dual RNA-Seq Analysis Pinpoints a Balanced Regulation between Symbiosis and Immunity in Medicago truncatula-Sinorhizobium meliloti Symbiotic Nodules

Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

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