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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.

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Gene Conversion

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

Gene Conversion

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

Chromosome Duplication

Chromosome Duplication

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...

Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...

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Updated: Jun 4, 2026

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

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Published on: June 28, 2013

An ILP solution for the gene duplication problem.

Wen-Chieh Chang¹, Gordon J Burleigh, David F Fernández-Baca

¹Department of Computer Science, Iowa State University, Ames 50011, USA. wcchang@iastate.edu

BMC Bioinformatics

|February 24, 2011

Summary

This summary is machine-generated.

We developed the first exact integer linear programming (ILP) method to solve the gene duplication (GD) problem. This approach accurately reconstructs species phylogenies from large gene family datasets, offering new genomic insights.

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Area of Science:

Phylogenetics
Computational Biology
Genomics

Background:

The gene duplication (GD) problem aims to infer a species tree with minimal gene duplication events.
Accurate species trees are crucial for understanding evolution, especially with complex gene families.
Existing methods for the NP-hard GD problem often rely on heuristics without performance guarantees.

Purpose of the Study:

To present the first exact integer linear programming (ILP) formulation for the gene duplication problem.
To demonstrate the scalability and accuracy of this novel ILP approach for phylogenetic inference.

Main Methods:

Developed an integer linear programming (ILP) formulation to solve the gene duplication problem exactly.
Validated the ILP approach using simulations on problem instances up to 14 taxa.
Applied the ILP method to a large-scale dataset of 6,084 genes from 12 seed plant taxa.

Main Results:

The ILP formulation successfully solved gene duplication problems for instances with up to 14 taxa.
Analysis of the seed plant phylogeny yielded an optimal solution placing Gnetales sister to conifers.
This represents a novel, large-scale genomic perspective on a key question in plant systematics.

Conclusions:

The ILP method provides an exact solution for the NP-hard gene duplication problem.
It can optimally solve instances with up to 14 taxa and 1,000 genes within hours, marking a significant advancement.
This work enables large-scale genomic insights into phylogenetic questions previously limited by heuristic estimations.