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ABSTRACT: Deciphering the Intricate Regulatory Network of Rust (Uromyces viciae-fabae) Resistance in Lentil (Lens culinaris Medik.) Through Comparative RNA-Seq Analysis

PROVIDER: PRJNA1061346 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27458543_1.fastq.gz	Fastqsanger.gz
	SRR27458543_2.fastq.gz	Fastqsanger.gz
	SRR27458544.fastq.gz	Fastqsanger.gz
	SRR27458544_1.fastq.gz	Fastqsanger.gz
	SRR27458544_2.fastq.gz	Fastqsanger.gz

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Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

Project description:Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.

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Genome-wide identification and tissue-specific profiling of microRNAs in lentil (Lens culinaris Medik.)

Project description:MicroRNAs (miRNAs) are key post-transcriptional regulators that influence plant development, metabolism, and stress adaptation. Despite the agronomic importance of lentil (Lens culinaris Medik.), its miRNA landscape remains poorly characterized. This study aimed to establish a comprehensive, tissue-specific atlas of conserved and novel miRNAs to improve understanding of gene regulation in lentil. Small RNA libraries from seven tissues—root, shoot, stem, mature leaf, flower, flower bud, and young pod—were sequenced using the Illumina HiSeq platform, generating over 432 million reads. A total of 1,490 miRNA candidates were identified, comprising 415 conserved and 1,075 novel miRNAs. Among 370 miRNAs with sufficient expression for analysis, 61% showed significant tissue-dependent variation, revealing extensive spatial regulation. Conserved miRNAs such as miR156, miR159, miR164, and miR172 displayed expression patterns consistent with their known developmental roles, whereas most novel miRNAs exhibited tissue-restricted accumulation, particularly in roots and reproductive organs. Predicted target and enrichment analyses indicated that conserved miRNAs primarily regulate transcription factors and hormone signaling components, while novel miRNAs are associated with redox homeostasis, lipid metabolism, and transport processes. This study provides the first comprehensive overview of miRNA expression in lentil, revealing a dual-layer regulatory architecture comprising conserved miRNAs that coordinate core developmental pathways and novel miRNAs that fine-tune tissue-specific and adaptive responses. The expanded lentil miRNA repertoire established here represents a valuable resource for future studies in legumes, including functional, evolutionary, and breeding-related applications.

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Genome-wide identification and tissue-specific profiling of microRNAs in lentil (Lens culinaris Medik.)

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Project description:Lentils (Lens culinaris) are produced in diverse agroecological regions and are consumed as one of the most important food legumes at world-wide. Lentils possess a nutritional profile from a human health perspective that is not only nutrient-dense but also offers a better balance between protein and carbohydrates. However, lentil causes food allergy which has been a significant concern due to increased consumption in parts of the world. Len c3, a none-specific Lipid Transfer Protein (LTP), was identified as one of the allergens in lentil seeds. In this study, we firstly identified the Len c3 encoding gene LcLTP3b via peptide sequence blasting. We then focused on screening natural variations to search for lentil germplasms that harbors natural mutated allergen-encoding genes. A natural variation 11 was identified with mutations at LcLTP3b and low accumulation of vicilin through genomic-assisted approaches. Furthermore, we generated a pool of lentil germplasms with Len c3-free background through crossing the identified natural variation 11 with two lentil cultivars, CDC Redmoon and CDC Gold. These Len c3-free lentil germplasms can be used as a breeding resource targeting at reducing allergen risk in lentil consumption.

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