Author Summary | This difference leads to important differences in the process of de novo genome assembly from short fragments of DNA. |
Author Summary | This set of methods is useful for the de novo assembly of compleX, polyploid genomes such as sugarcane, switchgrass, and Wheat. |
Discussion | Because genotypes being sequenced for de novo assembly of important crop species are usually chosen from a pool of bred cultivars, the recurrent cycles of crossing and selection make expectations about allele dosage distribution nontrivial. |
Discussion | This is crucial for de novo assemblies of polyploid genomes, which are naturally more fragmented due to genomic complexity. |
Discussion | Such a conservative model that performs well on high coverage situations is naturally suited to a newly assembled genome, where large numbers of reads are usually available due to the difficulty of de novo assembly. |
Estimated Ploidy | Bars represent the frequency of each ploidy estimated by ConPADE, for a set of 16,684 wheat contigs from the de novo assembly of chromosome arm 5D. |
Introduction | Complete genome de novo sequencing and assembly is a major initial step in understanding the underlying genetic architecture of important traits in any species [1—3]. |
Simulations | Because a coverage level of 50X resulted in correct estimated ploidies and high dosage estimation accuracy in the previous simulation sets, while still being viable in practice for de novo genome assembly efforts, we chose this value for more detailed simulations regarding contig lengths, the results of which are shown in Fig 5 and S5 Table. |
Wheat Dataset | Because of its size and complexity, a draft sequence of the wheat genome was created by sequencing and assembly of isolated chromosome arms, instead of a complete de novo genome assembly. |
Abstract | IEGs are known to be capable of induction without de novo protein synthesis. |
Introduction | Immediate-early (or primary response) genes are induced in response to a stimulus without the requirement of de novo protein synthesis [1]. |
Introduction | Necessarily, there is a delay in the expression of SRGs since, unlike IEGs, they require de novo protein synthesis. |
Introduction | The attenuation of the initial response of delayed IEGs to EGF was also shown to depend on negative feedback through de novo transcription in HeLa cells [10], but it is unknown whether negative feedback plays roles in other cell types or under other stimuli. |
The early peak signature is enriched for lEGs and signalling pathways | However, to qualify as an IEG these genes must be expressed without de novo protein synthesis. |
Comparison with NMR: Local structural propensities and long-range ordering | Nonetheless, the ability of PRE experiments to provide ensemble-averaged distance information between site-specific spin labels and all protons in the protein is extremely valuable for global validation of atomistic ensembles from de novo simulations. |
Comparison with NMR: Local structural propensities and long-range ordering | We note that it is highly nontrivial for de novo atomistic simulations to generate well-con-verged ensembles for a 61-residue IDP like p53-TAD With nontrivial structures and achieve a high level of agreement With NMR on both secondary and long-range structural features. |
Discussion | Coupled With appropriate structural and biophysical experiments, de novo atomistic simulations could provide a general framework for comparatively assessing the effects of disease-related mutations as well as post-translational modifications on IDP structure and interaction. |
Introduction | A possible strategy to overcome this fundamental limitation is to leverage significant recent advances in physics-based protein force fields and enhanced sampling techniques to calculate de novo structural ensembles [10,17]. |
Introduction | An important caveat is, however, de novo ensembles will inevitably contain artifacts due to persisting limitations in the current protein force fields as well as conformational sampling capability. |