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ABSTRACT: RNA-seq for DEG of SAW1 in lettuce

PROVIDER: PRJNA843589 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19444052_1.fastq.gz	Fastqsanger.gz
	SRR19444052_2.fastq.gz	Fastqsanger.gz
	SRR19444053_1.fastq.gz	Fastqsanger.gz
	SRR19444053_2.fastq.gz	Fastqsanger.gz
	SRR19444054_1.fastq.gz	Fastqsanger.gz

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Inflorescence development and the role of LsFT in regulating bolting in lettuce (Lactuca sativa L.)

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High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.)

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Transcript analysis under calcium deficiency in 6 day old Marchantia polymorpha wildtype (Tak-1) and Gβ-null mutant (gpb1-2) gemmalings and inter-species comparison of M. polymorpha, Arabidopsis and lettuce under calcium deficiency

Project description:Calcium deficiency response in liverwort, Arabidopsis and lettuce: (1) Marchantia polymorpha: M. polymorpha wildtype and Gβ-null mutant plants (Tak-1, gpb1-2) were grown in control liquid Yamagami media (2 mM Ca) for 6 days. For RNA-seq experiments, 6 day old gemmalings were transferred to calcium deficiency (0 mM Ca) media. Samples were collected at 48 h after the transfer. The transcriptomic profiles were collected from two independent batches. In total four biological replicates were used for each condition and each genotype for a total of 16 samples. (2) Arabidopsis thaliana: For Arabidopsis RNA-seq experiment, 6-day old seedlings grown on ½ strength MS media with sucrose were transferred to Yamagami media with 2 mM or 0 mM CaCl2 and treated for 7 days. (3) Lactuca Sativa: For lettuce RNA-seq, 4-day old seedlings grown on water agar (1%) were transferred to Yamagami media with 2 mM or 0.15 mM CaCl2 and treated for 7 days. In total four and three biological replicates were used for each condition for a total of 8 and 6 samples respectively for Arabidopsis and lettuce.

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Systematic identification and analysis of light-responsive circular RNA and co-expression networks in lettuce (Lactuca sativa)

Project description:Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA–microRNA–mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs’ biological mechanisms in light-treated plants.

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