Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18671450_1.fastq.gz | Fastqsanger.gz | |||
| SRR18671450_2.fastq.gz | Fastqsanger.gz | |||
| SRR18671451_1.fastq.gz | Fastqsanger.gz | |||
| SRR18671451_2.fastq.gz | Fastqsanger.gz | |||
| SRR18671452_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
2021-03-29 | GSE168886 | GEO
Project description:The small RNAs and their targets were characterized in lettuce (Lactuca sativa) genome by deep sequencing the small RNA populations of leaf tissues (cv. Salinas, Cobham and Diana), inoculated with Bremia and mock. The small RNA targets were also validated using PARE/degradome data derived from the same tissues.
2017-04-13 | GSE84280 | GEO
Project description:Increasing evidence of Pseudomonas aeruginosa on fresh plant-based foods raises food safety concerns. While internalization of pathogens such as Salmonella enterica in vegetables such as lettuce is well documented, corresponding data for P. aeruginosa are lacking. Moreover, climate change-associated temperature shifts may influence the plant microbiota and the presence of human pathogens. This study investigates the internalization and temperature-dependent gene expression of P. aeruginosa PAO1 on green oak leaf lettuce as a model system. For this purpose, oak leaf lettuce was cultivated in soil inoculated with P. aeruginosa PAO1_sfGFP_UHH07, and internalization was analyzed using confocal laser scanning microscopy. Temperature-dependent transcriptomic changes of P. aeruginosa PAO1 were assessed by analyzing differentially expressed genes following plant inoculation and incubation at 18 and 22 °C, respectively. P. aeruginosa PAO1 is capable of internalizing into the roots of oak leaf lettuce, but a translocation into leaves was not detected. Transcriptomic analyses showed that a moderate temperature increase shifts bacterial gene expression, with virulence genes upregulated at 22 °C and persistence-associated genes predominating at 18 °C. These results show that temperature influences the persistence and pathogenic potential of P. aeruginosa present on oak leaf lettuce, highlighting potential impacts of climate change on food safety.
2026-03-15 | GSE324477 | GEO
Project description:Lettuce (Lactuca sativa L.) is a highly perishable horticultural crop with a relatively short shelf life due to leaf senescence that limits its commercial value and contributes to food waste. Postharvest senescence varies with influences of both environmental and genetic factors. Preharvest genetic factors can be indicative of postharvest quality. Discovery of additional preharvest markers to assess lettuce shelf life is an important step towards increasing the efficiency of lettuce breeding efforts for improved shelf life. We selected and evaluated three romaine lettuces with variable shelf lives with the aim of identifying preharvest markers of lettuce postharvest shelf life. We evaluated leaf morphological characteristics for each of the three cultivars. To assess molecular indicators of shelf life, we used an RNA sequencing approach to construct transcriptomic profiles of two of the cultivars, a short shelf life (SSL) breeding line 60184 and a long shelf life (LSL) cultivar ‘Okeechobee’ at maturity. We identified 552 upregulated and 315 downregulated differentially expressed (DE) genes between the genotypes. We found that 27 % of the DE lettuce genes had an Arabidopsis thaliana ortholog characterized as senescence-associated, indicating that variable expression of senescence-associated genes (SAGs) could serve as a tool for preharvest markers of postharvest shelf life. Notably, we identified several SAGs and functional groupings with highly differential expression between the cultivars. This includes several jasmonate ZIM-domain (JAZ), jasmonic acid (JA) signaling genes, chlorophyll a-b binding (CAB) chloroplast-associated genes, and cell wall modification genes including pectate lyases (PL) and expansins (EXP). This study presented an innovative approach for identifying molecular markers for preharvest factors linked to postharvest traits for prolonged shelf. These genes could potentially be developed further as preharvest predictors of shelf life for lettuce breeding
2024-02-27 | GSE226302 | GEO
Project description:The draft genome of L. sativa (lettuce) cv. Tizian was sequenced in two Illumina sequencing runs, mate pair and shotgun. This entry contains the RAW sequencing data.
2018-02-09 | E-MTAB-6347 | biostudies-arrayexpress
Project description:The widespread use of chemical inputs in agriculture has raised concern over their long-term environmental and health impacts, driving demand for sustainable, natural product-based alternatives. Peptide-hormone signaling interactions, particularly those regulating senescence, are promising targets for developing such alternatives to advance postharvest technologies. However, most current insights stem from model species, limiting their translation to crops and ornamental plants. This study identifies the CLAVATA3/EMBRYO-SURROUNDING REGION-related (CLE) family CLE12 peptide (CLE12p) in Lactuca sativa as a peptide that shows potential for postharvest management of crops and ornamental flowers. CLE12p interacts with salt (NaCl), abscisic acid (ABA) and ethylene pathways, influencing lettuce development and morphology. Notably, CLE12p induced stomatal closure in a similar manner to that of ABA, suggesting overlapping signalling pathways. Transcriptomic analyses revealed how CLE12p modulates immune and defence responses, fluid transport, and leaf senescence, indicating a broader role in leaf senescence regulation similar to that of ethylene. Functionally, CLE12p delayed senescence in lettuce by preserving leaf greenness and water content following dark treatment and harvest. Additionally, CLE12p extended the longevity of cut roses by maintaining fresh weight and water content. These findings demonstrate the practical potential of CLE peptides in non-model species and support their application as natural tools for extending postharvest shelf life in crops and ornamental plants, paving the way for further exploration of their role in agricultural biotechnology.
2025-11-18 | GSE299676 | GEO
Project description:This study utilized the HIT-ISOseq method for high-throughput sequencing of RNA isoforms across multiple lettuce samples, generating millions of long reads per PacBio Sequel II SMRT Cell. Analysis of six tissue types revealed tissue-specific gene expression and RNA isoforms, facilitating updates to the lettuce reference genome annotation with expanded functional annotations.
2024-05-23 | GSE264560 | GEO
Project description:Transcriptome profiles in leaf lettuce
| PRJDB8725 | ENA
Project description:Lettuce is one of most consumed vegetables globally. This crop is susceptible to abiotic stresses. To understand the molecular mechanisms of stress response in lettuce, global transcriptome analysis was conducted. This analysis revealed distinctive temporal expression patterns among the stress-regulated genes in lettuce plants exposed to abiotic stresses
2023-09-01 | GSE241604 | GEO