Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 24, 2023

Abstract Background Domestic goose breeds are descended from either the Swan ( Anser cygnoides ) or Greylag anser ), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates thorough identification of genetic variations, thereby deepening our comprehension molecular mechanisms underlying diversity variability. Results To comprehensively facilitate population genomic pan-genomic analyses geese, we embarked on task 659 geese whole genome resequencing data compiling database 155 RNA-seq samples. By constructing for generated non-reference contigs totaling 612 Mb, unveiling collection 2,813 novel genes pinpointing 15,567 core genes, 1,324 softcore 2,734 shell 878 cloud genomes. Furthermore, detected an 81.97 Mb region showing signs selection, encompassing TGFBR2 gene correlated with weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) presence-absence variation revealed significant associations various meat quality, reproductive, composition For instance, encoding SVEP1 protein was linked to carcass oblique length, distinct gene-CDS haplotype exhibited length. Notably, analysis enrichment variable “hair follicle maturation” Gene Ontology term, potentially selection feather-related traits A suggested reduced frequency associated “regulation heart contraction” domesticated compared their wild counterparts. Our study provided insights into expression features functions by integrating patterns across multiple organs tissues analyzing variation. Conclusion This accomplishment originates discernment multitude signals candidate wide array traits, markedly enhancing understanding processes domestication breeding Moreover, assembling has yielded comprehensive apprehension genome, establishing it as indispensable asset poised offer innovative viewpoints make substantial contributions future initiatives.

Language: Английский

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Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference

Life, Journal Year: 2023, Volume and Issue: 13(6), P. 1360 - 1360

Published: June 9, 2023

A pangenome is a collection of the common and unique genomes that are present in given species. It combines genetic information all sampled, resulting large diverse range material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, not bound by physical constraints single genome, so it can capture more variability. Thanks introduction concept pangenome, possible use exceedingly detailed sequence data study evolutionary history two different species, or how populations within species differ genetically. In wake Human Pangenome Project, this review aims at discussing around human variation, which then framed pangenomic inform population genetics, phylogenetics, public health policy providing insights into basis diseases determining personalized treatments, targeting specific profile an individual. Moreover, technical limitations, ethical concerns, legal considerations discussed.

Language: Английский

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RepeatOBserver: tandem repeat visualization and centromere detection

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 30, 2023

Abstract Tandem repeats can play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination, and the regulation of gene activity. There is a growing need for bioinformatics tools that visualize explore chromosome-scale repeats. Here we present RepeatOBserver, new tool visualizing tandem clustered transposable elements identifying potential natural locations, using Fourier transform walks: https://github.com/celphin/RepeatOBserverV1 . RepeatOBserver identify broad range (3-20, 000bp long) genome assemblies without any priori knowledge repeat sequences or optimizing parameters. allows easy visualization positions both perfect imperfect repeating across each chromosome. We use to compare walks, patterns wide well-studied species (e.g., human, mouse-ear cress), crops, non-model organisms fern, yew). Analyzing 107 chromosomes with known positions, find centromeres consistently occur regions have least diversity types (i.e. one few repeated are very high numbers). Taking advantage this information, genomic Shannon index predict locations several other assemblies. The spectra produced by help historic neocentromeres, retrotransposon clusters copy variation. Identification split inverted at inversion boundaries suggests some chromosomal inversions misassemblies be predicted RepeatOBserver. therefore flexible comprehensive characterization used variety interest

Language: Английский

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Are Viruses Taxonomic Units? – A Protein Domain and Loop-Centric Phylogenomic Assessment

Published: June 6, 2024

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by phylogenetic analysis aligned genomic or metagenomic sequences. Taxonomic assumed independent organizational, functional evolutionary that follow ‘natural’ historical rationale. Here, I use phylogenomic other arguments show not self-standing genetically-driven biological systems. Instead, they crucial components holobionts, organization dynamically integrate the genetics, epigenetic, physiological properties their co-evolving members. Remarkably, analyses share protein domain loop structures with cells throughout history via massive processes reticulate evolution, helping spread innovations across wider spectrum. Thus, merely MGEs microbes. genomes proteomes conduct cellularly integrated akin those cataloged GO Consortium. This prompts generation compositional hierarchies replace ‘is-a-kind-of’ ‘is-a-part-of’ logic better describe mereology cellular viral makeup. My demands new paradigm integrates virus modern evolutionarily centered organisms.

Language: Английский

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Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9271 - 9271

Published: Aug. 27, 2024

The economic significance of ruminants in agriculture underscores the need for advanced research methodologies to enhance their traits. This review aims elucidate transformative role pan-omics technologies ruminant research, focusing on application uncovering genetic mechanisms underlying complex traits such as growth, reproduction, production performance, and rumen function. Pan-omics analysis not only helps identifying key genes regulatory networks associated with important but also reveals impact environmental factors trait expression. By integrating genomics, epigenomics, transcriptomics, metabolomics, microbiomics, enables a comprehensive interplay between genetics factors, offering holistic understanding We explore specific examples where these have been pivotal, highlighting identified through approaches. Additionally, we trace historical evolution each omics field, detailing progression from foundational discoveries high-throughput platforms. provides critical synthesis recent advancements, new insights practical recommendations industry. broader implications modern animal husbandry are discussed, emphasizing potential drive sustainable improvements systems.

Language: Английский

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