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REPOSITORIES: ENA
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Project description:<p><strong>BACKGROUND:</strong> Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value.</p><p><strong>FINDINGS:</strong> Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2 and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified.</p><p><strong>CONCLUSIONS:</strong> Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.</p>
2022-05-18 | MTBLS3657 | MetaboLights
Project description:Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generated a de novo genome assembly and genome-wide transcript expression data for Kalanchoe fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identified signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
2018-01-09 | MTBLS519 | MetaboLights
Project description:Complete genome sequencing of the new proposed species Clavibacter lycopersicum
| PRJNA747289 | ENA
Project description:The complete genome sequence of Enterobacter roggenkampii, OIPH-N260
| PRJDB10185 | ENA
Project description:Complete genome sequence of three Streptococcus species
| PRJDB10330 | ENA
Project description:Title:Complete Genome Sequence, Biological Activities, and Metabolomic Profiles of Mangrove-derived Streptomyces sp. SM1P Author: Risa Nofiani, Puji Ardiningsih, Rizky, Cantika Dylani Putri, Rifa Rakayati, Rudiyansyah, Elfahmi, Syamsurizal, Agus Sukito, Ario Betha Juanssilfero, Josephine Elizabeth Siregar, Andita Fitri Mutiara Rizki, Wihda Aisarul Azmi, Alexandra J. Weisberg, Taifo Mahmud
| MSV000095970 | GNPS
Project description:Title:Complete Genome Sequence, Biological Activities, and Metabolomic Profiles of Mangrove-derived Streptomyces sp. SM1P
Author: Risa Nofiani, Puji Ardiningsih, Rizky, Cantika Dylani Putri, Rifa Rakayati, Rudiyansyah, Elfahmi, Syamsurizal, Agus Sukito, Ario Betha Juanssilfero, Josephine Elizabeth Siregar, Andita Fitri Mutiara Rizki, Wihda Aisarul Azmi, Alexandra J. Weisberg, Taifo Mahmud7
| MSV000095967 | GNPS
Project description:Enterobacter asburiae L1 Complete Genome Sequencing
| PRJNA243408 | ENA