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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Related Experiment Video

Updated: Jun 4, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Exploring intra- and intergenomic variation in haplotype-resolved pangenomes.

Eef M Jonkheer1,2, Dick de Ridder1, Theo A J van der Lee2

  • 1Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands.

Plant Biotechnology Journal
|January 5, 2025
PubMed
Summary

Researchers developed PanTools, a novel software package for analyzing plant pangenomes. This tool enhances the exploration of complex, phased genomes, particularly polyploids, revealing significant genetic diversity and aiding in the detection of genomic variations.

Keywords:
genetic variationgenome evolutiongenome organizationhaplotype‐resolved genomespangenomicsvisualization

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Haplotype-resolved (phased) genome assemblies are increasingly prevalent in plant genomics due to advances in sequencing.
  • Existing computational tools struggle to effectively analyze these phased genomes, especially for polyploid species.

Purpose of the Study:

  • To introduce PanTools, a novel software package designed for analyzing phased genome assemblies.
  • To enhance the exploration of intra- and intergenomic variation within plant pangenomes, including polyploids.

Main Methods:

  • Developed a pangenome approach by updating the graph representation and adding functionalities to PanTools.
  • Incorporated features to assess synteny, gene retention, repeat profiling, and mutation rates (synonymous and nonsynonymous).
  • Constructed and analyzed pangenomes for potato (diploid and tetraploid) and apple (diploid) species.

Main Results:

  • PanTools successfully analyzed diploid and tetraploid potato and diploid apple pangenomes.
  • High intra- and intergenomic allelic diversity was observed, including gene presence/absence, SNPs, indels, and structural variants.
  • New functionalities proved effective in identifying introgressions and potential misassemblies in phased genomes.

Conclusions:

  • PanTools provides essential capabilities for exploring complex phased plant genomes, particularly polyploids.
  • The software facilitates the discovery of genetic diversity and aids in quality control of genome assemblies.
  • PanTools is publicly available, supporting further research in plant genomics.