Linseed genome assembly
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB87373 | ENA |
REPOSITORIES: ENA
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Project description:The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health.
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Project description:<p><strong>BACKGROUND:</strong> Traditional Chinese medicine has used <em>Peucedanum praeruptorum</em> Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and, thus, the development of better breeding strategies.</p><p><strong>RESULTS:</strong> The authors assembled a telomere-to-telomere genome by combining PacBio HiFi, ONT ultra- long and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes and genome completeness >98%. Comparative genomic analysis suggested that <em>P. praeruptorum</em> experienced two WGD events like the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the <em>COSY</em> and cytochrome <em>P450</em> genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.</p><p><strong>CONCLUSIONS:</strong> The authors obtained a T2T genome for <em>P. praeruptorum</em>, which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.</p>
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Project description:The goal of the study is to identify gene expression during seed development process in linseed flax.
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Project description:The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health. The experiment was carried out in a complete randomized blocked designed structure comprising 14 Holstein-Friesian cows (6 second parity, 2 third parity and 6 older cows), selected from a 550-cow herd. Cows were paired in 7 blocks on the basis of similarity in parity (second parity, third parity and older cows), expected date of calving, and milk performance in the previous lactation (in order of priority). Cows within each block were randomly allocated to one of two treatment groups, “Omega” or “Control”. The dietary Omega treatment consisted of a basal diet supplemented with a concentrate-mixture including linseed on a dry matter (DM) basis, whereas cows in treatment group Control were supplemented with a concentrate mixture without linseed. Linseed was chosen because it is rich in c9,c12,c15-18:3 (ALA). Concentrate mixtures were fed with a concentrate dispenser. Experimental treatments started 3 weeks before the expected calving date (wk -3) and lasted until 6 weeks after calving (wk 6).
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