Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1087263 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:<p><strong>BACKGROUND:</strong> Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.</p><p><strong>FINDINGS:</strong> We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.</p><p><strong>CONCLUSIONS:</strong> Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.</p>
2020-12-04 | MTBLS1983 | MetaboLights
Project description:The Colorado potato beetle (CPB) is a major pest of potato crops that has evolved resistance to more than 50 pesticides. For decades, CPB has been a model species for research on insecticide resistance, insect physiology, diapause, reproduction and evolution. Yet, the research progress in CPB is constrained by the lack of comprehensive genomic and transcriptomic information. Here, building on a recently established chromosome-level genome assembly, we built a gene expression atlas of the CPB using the transcriptomes of 61 samples representing major organs and developmental stages. By using both short and long reads, we improved the genome annotation and identified 6,623 more genes that were missed in previous annotations. We then established a web portal allowing the search and visualization of the gene expression atlas for the research community. The CPB atlas provides useful tools and comprehensive gene expression data, which will accelerate future research in both pest control and insect biology fields.
2025-01-07 | GSE285883 | GEO
Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.
2020-11-03 | PXD021036 | Pride
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
| 2140168 | ecrin-mdr-crc