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Metagenomes from the Bedford Basin and the Scotian shelf

ABSTRACT: Metagenomes from the Bedford Basin and the Scotian shelf Metagenome

PROVIDER: PRJNA725221 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14596400_1.fastq.gz	Fastqsanger.gz
	SRR14596400_2.fastq.gz	Fastqsanger.gz
	SRR14596401_1.fastq.gz	Fastqsanger.gz
	SRR14596401_2.fastq.gz	Fastqsanger.gz
	SRR14596402_1.fastq.gz	Fastqsanger.gz

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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

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Metagenomes from the Bedford Basin and the Scotian shelf

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