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Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Updated: May 27, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Simultaneous structural variation discovery among multiple paired-end sequenced genomes.

Fereydoun Hormozdiari¹, Iman Hajirasouliha, Andrew McPherson

¹School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Genome Research

|November 4, 2011

Summary

This study introduces a new method for simultaneous structural variation discovery from whole-genome shotgun sequencing (WGSS) data. The novel approach improves accuracy by reducing false de novo variations and identifying more true variations compared to conventional methods.

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Published on: June 23, 2012

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Whole-genome shotgun sequencing (WGSS) is increasingly popular for comparative genomic studies.
Conventional comparative genome variation studies involve a two-step process: individual genome comparison to a reference, followed by inter-genome comparison.
This conventional approach can lead to inaccuracies, including high numbers of false de novo variations and missed true variations.

Purpose of the Study:

To develop a novel, more accurate framework for structural variation detection in multiple high-throughput sequenced genomes.
To introduce a maximum parsimony-based simultaneous structural variation discovery problem and provide efficient algorithms.

Main Methods:

Developed a novel framework for simultaneous structural variation discovery from multiple WGSS datasets.
Introduced a maximum parsimony-based approach for this problem.
Applied and compared the novel framework against the conventional method using Yoruban and CEU trios.

Main Results:

The proposed simultaneous framework significantly reduces the number of incorrectly predicted de novo variations.
The novel method successfully identifies more known (true) structural variations compared to the conventional approach.
Observed inaccuracies in the conventional framework, such as an unexpectedly high number of de novo variations in children relative to parents.

Conclusions:

Simultaneous structural variation discovery offers higher accuracy than conventional two-step methods.
The proposed maximum parsimony-based framework enhances the reliability of comparative genomic variation studies.
This advancement is crucial for accurate population genetics and phenotype-based genomic research.