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Genome - Crossref

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Last Updated: 03 September 2022

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A thousand-genome panel retraces the global spread and climatic adaptation of a major crop pathogen

Human activities influence the evolutionary history of many species of earth. predicting crop pathogens' future impacts is crucial to knowing how pathogens maintain control techniques and cope with new environments. Here, we discuss this by assembling a global thousand-genome panel of Zymoseptoria tritici, a common fungal pathogen of wheat identified in many production regions around the world. Our research reveals how large population genomic panels have aided in new insight into a common crop pathogen's evolutionary history.

Source link: https://doi.org/10.1101/2022.08.26.505378


Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

Synthetic hexaploid wheat is grown from an interspecific cross between durum wheat and goat grass and has been reported to have significant novel alleles-controlling biotic and abiotic stress resistance. During drought stress, we discovered 90 novel MTAs and haplotype blocks associated with grain yield and yield-related characteristics, including root characteristics under drought stress. The large number of MTAs identified on the D-genome have shown the promise of SHWs for elucidating complex traits' genetic architecture and providing an opportunity for further improvement of wheat under rapidly changing climatic conditions.

Source link: https://doi.org/10.3390/ijms19103011


Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation

The Japanese eel, European eel, and American eel are migratory, temperate zone fish with several common life cycle traits. Panmixia in these eel species has already been investigated by the population genetics. It was found that a Japanese eel group from Kuma River differed from other populations of the same species. The life cycle of the Japanese eel is well-established, and the Kuma River is in the center of the species's habitat.

Source link: https://doi.org/10.3390/genes9100474


Genome-Wide Mapping and Microscopy Visualization of Protein–DNA Interactions by pA-DamID

The key benefits of pA-DamID include a fast and simple analysis of DNA that is associated with the protein of concern, objective mapping of proteinu2013DNA interactions, and the ability to isolate cell subpopulations by flow cytometry before further sample processing. pA-DamID is particularly useful for analyzing proteins that compose large chromatin domains or that are part of specific nuclear systems, such as the nuclear lamina. paraphrasedoutput sequencing libraries from cell harvesting to the preparation of microscopy slides and high-throughput sequencing libraries are described in this chapter.

Source link: https://doi.org/10.1007/978-1-0716-2140-0_12


Estimating Global Methylation and Erasure Using Low-Coverage Whole-Genome Bisulfite Sequencing (WGBS)

Although WGBS is prohibitively costly for experiments involving many samples, low-coverage WGBS can accurately determine global methylation and erasure at similar prices to high-performance liquid chromatography or enzyme-linked immunosorbent assays. Here we'll go into detail about the effectiveness of low-coverage WGBS using empirical bootstrap samplers and quantitative estimators similar to those used in election polling in lieu of describing a WGBS library construction and quantitation approach.

Source link: https://doi.org/10.1007/978-1-0716-1294-1_3


Genome as (hyper)text: From metaphor to theory

Abstract: Since molecular genetics was first developed, the correspondence between language and genetic information exchange processing has been recognized. A text should be regarded as an artefact of knowledge creation, dissemination, conservation, and transformation of knowledge. A general theory of text should be able to describe linguistic texts and their evolution, operation, and change. It should also be possible to describe a genome's biochemical system as a hypertext that includes an ordered subset of other texts. A text can be considered a quasi-organism with memory, creative-cognitive, and communicative power, while a cell can be classified as a quasi-intelligence capable of manipulating abstract semiotic entities.

Source link: https://doi.org/10.1515/sem-2016-0214


High-resolution structural variation catalogue in a large-scale whole genome sequenced bovine family cohort data

SVs play a disproportionally large role in gene expression, according to recent human expression QTL mapping results, underlining the importance of including SVs in genetic analyses. Hence, this research was designed to produce and examine a high-quality bovine SV catalogue utilizing unique cattle family cohort data. Of these, we established a subset of copy number variants in an independent cohort, proving that at least 80% of the CNVs are true variants, segregating in the population. We also established a subset of copy number variants using a direct genotyping technique. Although most of the correctly genotyped CNVs are tagged by single nucleotide polymorphisms established in WGS results, most CNVs were not identified by individual SNPs obtained from a 50K genotyping array, the majority of which are properly genotyped CNVs were not identified by individual SNPs obtained from a 50K genotyping array. Conclusion We produced a high-quality SV catalog based on unique whole genome sequenced bovine family cohort results.

Source link: https://doi.org/10.21203/rs.3.rs-2007387/v1


Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

ABSTRACT: The majority of eukaryotic genes are composed of exons and introns, requiring the precise removal of introns from pre-mRNAs to allow protein biosynthesis. Analyzing 121 plant genome sequences based on their annotation revealed good splice site preservation across species, annotation mistakes, and true biological divergence from canonical splice sites. The frequency of non-canonical splice sites correlates strongly with their divergence from canonical ones, indicating either an accumulation of possibly neutral mutations or shift toward canonical splice sites. Strong conservation of multiple species and non-random accumulation of substitutions in splice sites both suggest a functional relevance of non-canonical splice sites. For 96. 7% for GT-AG, 1. 2% for AT-AC, 0. 06% for AT-AC, and 0. 09% for minor non-canonical splice sites, according to the average composition of splice sites across all investigated species. We conclude that bona fide non-canonical splice sites are present and appear to be functionally relevant in most plant genomes, even in low numbers.

Source link: https://doi.org/10.1101/428318


Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

Plant genome organization was addressed here by means of cloning and sequencing TE fragments of various types of Aegilops speltoides genome. Individual genotypes were analyzed cytogeneticically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization. The speltoides genome of the Triticeae tribe is found in a Triticeae tribe and has traces of evolutionarily distant species. Different TE clones displayed sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae at the chromosomal level.

Source link: https://doi.org/10.1155/2018/4373089


Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool

Abstract: Genome-scale metabolic simulations are both important tools for insilico phenotype prediction and strain optimisation. The initial draft is produced using published models as templates, prompting further curation. BiGG Integration Tool, a merlin user friendly version, takes such an approach. This tool uses BiGG Models database models as templates for the draft models. This paper's primary aim is to analyze the draft models created using this software and compare them to CarveMe models, both of which use the BiGG database and curated models. This review found that models created with BIT for each organism were differentiable, despite sharing a significant portion of metabolic functions. In all metrics, BIT had higher success than CarveMe. Hence, BIT can be considered a fast and reliable substitute for draft reconstruction for bacteria models.

Source link: https://doi.org/10.1515/jib-2022-0014

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions