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1,293 results for “gene sequencing”

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dryad36/100

Analyses of ergot alkaloid production in Aspergillus leporis and an easD knockout and sequences for phylogenetic analyses of rugulovasine-associated genes

Ergot alkaloids are fungal specialized metabolites that are important in agriculture and serve as sources of several pharmaceuticals. Aspergillus leporis is a soil saprotroph that possesses two ergot alkaloid biosynthetic gene clusters encoding lysergic acid amide production. We identified two additional, partial biosynthetic gene clusters within the A. leporis genome containing some of the ergot alkaloid synthesis (eas) genes required to make two groups of clavine ergot alkaloids, fumigaclavines and rugulovasines. Clavines possess unique biological properties compared to lysergic acid derivatives. Bioinformatic analyses indicated the fumigaclavine cluster contained functional copies of easA, easG, easD, easM, and easN. Genes resembling easQ and easH, which are required for rugulovasine production, were identified in a separate gene cluster. The pathways encoded by these partial, or satellite, clusters would require intermediates from the previously described lysergic acid amide pathway to synthesize a product. Chemical analyses of A. leporis cultures revealed the presence of fumigaclavine A. Rugulovasine was only detected in a single sample, however, prompting a heterologous expression approach to confirm functionality of easQ and easH. An easA knockout strain of Metarhizium brunneum, which accumulates the rugulovasine precursor chanoclavine-I aldehyde, was chosen as expression host. Strains of M. brunneum expressing easQ and easH from A. leporis accumulated rugulovasine as demonstrated through mass spectrometry analysis. These data indicate that A. leporis is exceptional among fungi in having the capacity to synthesize products from three branches of the ergot alkaloid pathway and for utilizing an unusual satellite cluster approach to achieve that outcome.

opencc-zeroJun 2023View details →

zenodo36/100

Massive Chinese domestic pigs provide missing sequences in reference genome and reveal non-coding sequence variations regulating gene expression across Eurasian boars

This dataset contains novel sequences in Chinese domestic pigs but is absent in Sscrofa 11.1 reference genome. The detailed information for each file is recorded in the README file.

opencc-by-4.0Jun 2023View details →

zenodo36/100

Sequences of target genes and probes for construction of exon-targeted libraries for Prunus spp.

(Files) "baits-selection-15171.fas": Sequences of 15,171 baits used for hybridization reaction. "Targets_mume.15171.xlsx": Sequences of target genes used for design baits.   (Protocol for bait design) To selectively retrieve libraries with exons, a myBaits Custom design kit was used to design 1–20-K probes (Arbor Biosciences, Ann Arbor, MI, USA), which uses biotinylated RNA probes to concentrate fragments carrying sequences of interest (Gnirke et al., 2009), based on the published genomic and coding sequences of P. mume (Zhang et al., 2012). We subjected 29,621 non-redundant coding loci to search for single hits with BLAST+ (MEGABLAST with -p 70) against the P. mume genome, for the subsequent bait design. A 120-mer bait with 25–55 GC% per locus was randomly designed for each locus, and finally we obtained a bait set targeting 15,171 coding loci.

opencc-by-4.0Jul 2023View details →

zenodo36/100

Models and Data associated with: Single-cell gene expression prediction from DNA sequence at large contexts

This archive holds trained models and associated data for the <a href="https://www.biorxiv.org/content/10.1101/2023.07.26.550634v1">manuscript</a>: "Single-cell gene expression prediction from DNA sequence at large contexts" Structure: <ul> <li>configs - example configs for the workflows to produce publication data </li> <li>data_* - pre-processed single cell data used for publication</li> <li>models_* - model checkpoints, hyperparameters and training progress in tensorboard logs</li> <li>preprocessing - additional data required to reproduce the pre-processing workflow</li> </ul>   "Copyright 2023 GlaxoSmithKline Research & Development Limited. All rights reserved."

opencc-by-nc-nd-4.0Sep 2023View details →

dryad36/100