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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...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

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.

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

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.

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...

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Related Experiment Video

Updated: Jan 10, 2026

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

PGDD 2.0: Plant Genome Duplication Database with updated content and tools.

Ankush Sharma^1,2, John E Bowers^1,2, Tae-Ho Lee³

¹Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, United States.

Nucleic Acids Research

|November 26, 2025

Summary

PGDD 2.0 enhances plant comparative genomics by integrating over 120 telomere-to-telomere genome assemblies. This updated database aids in understanding plant genome evolution, polyploidy, and gene duplication events with high precision.

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Last Updated: Jan 10, 2026

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

Plant genomics
Evolutionary biology
Bioinformatics

Background:

Polyploidy and gene duplication are major drivers of plant genome evolution.
Synteny and colinearity are crucial for evolutionary inference in plants.
Previous versions of the Plant Genome Duplication Database (PGDD) provided valuable resources.

Purpose of the Study:

To introduce PGDD 2.0, a significantly updated Plant Genome Duplication Database.
To provide a comprehensive resource for plant comparative genomics using telomere-to-telomere assemblies.
To develop new tools for visualizing and analyzing synteny and genome evolution.

Main Methods:

Aggregation of over 120 complete telomere-to-telomere (T2T) plant genome assemblies.
Standardized bioinformatic pipeline for calling syntenic blocks and estimating duplication times (Ks).
Development of interactive synteny networks, riparian alignment views, and an embedded SynVisio module.

Main Results:

PGDD 2.0 now includes >120 T2T assemblies across major Viridiplantae lineages.
New visualization tools enable detailed analysis of mesosynteny and rearrangements.
The database supports precise tracing of gene family evolution post-duplication.

Conclusions:

PGDD 2.0 is a user-centered platform accelerating discovery in plant polyploidy and genome evolution.
The database facilitates high-resolution analysis of ancient whole-genome duplication events.
Advances support detailed investigation of gene duplication fates and evolutionary trajectories.