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ABSTRACT: RNA-seq on different zones of Casparian strip defective mutant roots in Lotus japonicus

PROVIDER: PRJNA1083776 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28225106_1.fastq.gz	Fastqsanger.gz
	SRR28225106_2.fastq.gz	Fastqsanger.gz
	SRR28225107_1.fastq.gz	Fastqsanger.gz
	SRR28225107_2.fastq.gz	Fastqsanger.gz
	SRR28225108_1.fastq.gz	Fastqsanger.gz

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Project description:RNA-seq on Casparian strip defective mutant roots in Lotus japonicus

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Project description:The casparian strip serves as a crucial diffusion barrier in the endodermis, playing a vital role in controlling the flow of substances between the root and its external environment. Here, we observed that when the casparian strip is absent, bacteria can accumulate abundantly on the roots. To investigate the impact of this bacterial accumulation on the root indued by casparian strip deficiency , we inoculated Col-0 and sgn3 myb36 roots with CHA0 in a hydroponic system. Ultimately, we found that the bacterial accumulation on the roots, resulting from the absence of the Casparian strip, strongly induces the immune response of the roots. This indicates that the casparian strip plays an important role in regulating the interaction between the root and microorganisms.

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CASPARIAN STRIP INTEGRITY FACTOR 2 (CIF2) peptide induces SCHENGEN3 (SGN3) receptor-kinase dependent transcriptional changes

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Constitutive over-expression of LjMyb14 in Lotus japonicus.

Project description:To identify the regulatory targets of the R2R3-Myb transcription factor, LjMyb14, the gene was constitutively over-expressed in Lotus japonicus under the Lotus ubiquitin promoter. The gene expression levels of three biological replicates of the Lotus japonicus (MG20) were averaged and compared to the the gene expression levels of three independent lines of Lotus japonicus japonicus constituitively over expressing LjMyb14 using the Lotus ubiquitin promoter.

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Transcriptome profiling for wild-type, single and double mutants for Nuclear Factor YA1 (nf-ya1) and hypernodulation phenotype (har1) mutants in roots of Lotus japonicus

Project description:Acting in a partially redundant manner, NF-Ys were shown previously to regulate bacterial infection, including selection of a superior rhizobial strain, and to participate in mediating nodule structure formation. However, the exact mechanism(s) by which these transcriptional factors exert their symbiotic functions has remained elusive. Gene expression profiling for wild-type and Nuclear Factor YA (nf-ya)-A mutants in roots of Lotus japonicus were conducted 4 days after inoculation with Mesorhizobium loti in order to understand the interaction of NF-Ys and other genes in Lotus japonicus.

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Endodermis-specific Receptor-like Kinase (ERK1) is required for the deposition of lignin in the Casparian strip in the root

Project description:The Casparian strip constitutes a physical diffusion barrier formed by the polar deposition of lignin in the root endodermis. The polar deposition of lignin is thought to be mediated by the scaffolding activity of membrane bound Casparian Strip domain proteins (CASPs) and the dirigent domain-containing protein Enhanced Suberin1 (ESB1). Here, we show that the endodermis-specific receptor-like kinase (ERK1), is part of this machinery, playing an essential role in the localization of CASP proteins and in the deposition of lignin, which ultimately are required for the formation of afunctional Casparian strip. ERK1 is localized to the cytoplasm and nucleus of the endodermis, and is part of a signalling pathway that implicates the circadian clock regulator Time for Coffee (TIC). In addition, we found that loss of ERK1 and TIC disrupts the Casparian strip organisation and alters composition of the root microbiome.

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