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Related Concept Videos

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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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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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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Building Phylogenetic Trees From Genome Sequences With kSNP4.

Barry G Hall1, Jeremiah Nisbet1

  • 1Bellingham Research Institute, Portland, OR, USA.

Molecular Biology and Evolution
|November 10, 2023
PubMed
Summary
This summary is machine-generated.

kSNP4 software identifies single-nucleotide polymorphisms (SNPs) without a reference genome, enabling efficient phylogenetic tree construction from microbial genomes. This user-friendly tool simplifies complex analyses for researchers of all levels.

Keywords:
SNPskSNP4sequences

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analysis using whole genome sequences provides maximal information for resolving evolutionary relationships.
  • Single-nucleotide polymorphisms (SNPs) offer a powerful approach for phylogenetic inference, especially with large datasets like hundreds of microbial genomes, and bypass the need for genome alignments.

Purpose of the Study:

  • To introduce and provide a detailed protocol for kSNP4, a novel software tool for phylogenetic analysis.
  • To demonstrate the utility of kSNP4 in identifying SNPs and constructing phylogenetic trees from genome sequences without a reference genome.

Main Methods:

  • kSNP4 identifies SNPs directly from genome sequences, obviating the need for a reference genome or multiple sequence alignments.
  • The software implements parsimony, maximum likelihood, and neighbor-joining methods for phylogenetic tree estimation.
  • kSNP4 includes functionality for annotating identified SNPs and is a self-contained, command-line program.

Main Results:

  • kSNP4 successfully identifies SNPs and constructs phylogenetic trees from genome sequences.
  • The program is designed for ease of use, requiring no prior programming or bioinformatics expertise.
  • A comprehensive user guide is provided, detailing installation and all features of kSNP4.

Conclusions:

  • kSNP4 is an accessible and efficient tool for microbial phylogenetic analysis using genome-wide SNPs.
  • The software democratizes advanced phylogenetic methods, making them available to a broad range of users from students to senior researchers.
  • This protocol facilitates the adoption and application of kSNP4 for robust evolutionary studies.