Ontology highlight
ABSTRACT:
PROVIDER: PRJNA761673 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CVM NARMS Seafood
| PRJNA590891 | ENA
Project description:CVM NARMS Retail Seafood Isolates
| PRJNA800017 | ENA
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:Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. Two examples of TEs that escape this regulation are the murine-specific intracisternal A particle (IAP) elements Avy and AxinFu, which exhibit inter-individual variability in methylation associated with phenotypic variation. To determine the frequency of this phenomenon, its underlying mechanisms, and its effects on gene expression, we previously conducted a screen identifying variably methylated IAPs (VM-IAPs). Here, we fully validate these elements, categorising VM-IAPs for the first time into those exhibiting tissue specificity (tsVM-IAPs) and those showing uniform methylation among tissues (constitutive- or cVM-IAPs) with both types having the potential to regulate the genome in cis. Using our validated set of VM-IAPs, we explore how variable methylation is established and identify sequences enriched within cVM-IAPs, implicating genetics as a determinant of variability. CTCF, a methylation-sensitive transcription factor known for its role in facilitating chromatin interactions, is enriched at VM-IAPs and we show that CTCF binding is inversely correlated with methylation at cVM-IAPs. We uncover dynamic physical interactions between lowly-methylated cVM-IAPs and other genomic loci, suggesting that VM-IAPs have the potential for long-range genomic regulation. Lastly, screening for variably methylated regions in other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We propose that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs has the potential to cause inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
2021-03-02 | GSE159110 | GEO
Project description:We applied the RNA-Seq approach to reconstruct the transcriptome of Vitis vinifera cv. Corvina, using RNA pooled from a comprehensive set of sampled tissues in different organs and development steps, and we were able to reconstruct some novel and putative private Corvina genes. We analyzed the expression of these genes in three berry developmental conditions, and posit that they may play some role in the formation of the mature organ. Background: Plants display a high genetic and phenotypic variability among different cultivars. Understanding the genetic components that contribute to phenotypic diversity is necessary to disentangle genetic factors from the environment. Given the high degree of genetic diversity among plant cultivars a whole-genome sequencing and re-annotation of each variety is required but a reliable genome assembly is hindered by the high heterozigosity and sequence divergence. Results: we show the feasibility of an approach based on sequencing of cDNA by RNA-Seq to analyze varietal diversity between a local grape cultivar Corvina and the PN40024 grape reference genome. We detected 15,260 known genes and we annotated alternative splicing isoforms for 9,463 genes. Our approach allowed to define 2,321 protein coding putative novel genes in unannotated or unassembled regions of the reference genome PN40024 and 180 putative private Corvina genes whose sequence is not shared with the reference genome. Conclusions: With a de novo assembly based approach we were able to reconstruct a substantial part of the Corvina transcriptome and we improved substantially known genes annotations by better defining the structure of known genes, annotating splicing isoforms and detecting unannotated genes. Moreover our results clearly define sets of private genes which are likely part of the âdispensableâ genome and potentially involved into influencing some cultivar-specific characteristics. In plant biology a transcriptome de novo assembly approach should not be limited to species where no reference genome is available as it can improve the annotation lead to the identification of genes peculiar of a cultivar.
2012-07-30 | E-MTAB-4220 | biostudies-arrayexpress