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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 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.

Genomic DNA in Prokaryotes

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...

Evolution of Microbial Genome

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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...

Prokaryotic Gene Structure and Organization

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

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Updated: May 20, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

DNA-energetics-based analyses suggest additional genes in prokaryotes.

Garima Khandelwal¹, Jalaj Gupta, B Jayaram

¹Department of Chemistry, Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110 016, India.

Journal of Biosciences

|July 4, 2012

Summary

This study introduces a new method to find novel genes in prokaryotic genomes using DNA

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Prokaryotic genomes are complex and contain undiscovered genetic elements.
Identifying novel genes is crucial for understanding microbial function and evolution.

Purpose of the Study:

To develop a novel computational methodology for predicting previously unidentified genes in prokaryotic genomes.
To leverage inherent DNA energetics and protein properties for accurate gene prediction.

Main Methods:

Analysis of DNA thermodynamic stability to identify potential gene regions.
Filtering predicted regions using existing genomic annotations.
Assessing candidate genes based on protein stereochemical properties and SwissProt tripeptide frequencies.

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The Multifaceted Benefits of Protein Co-expression in Escherichia coli

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Main Results:

Successfully identified a reliable set of novel genes in prokaryotic genomes.
The methodology demonstrated effectiveness even in well-annotated genomes.
The approach is robust across varying GC-content, genome sizes, and annotated gene counts.

Conclusions:

The proposed method offers a powerful tool for prokaryotic gene discovery.
This energetic and property-based approach enhances the accuracy of novel gene prediction.
The methodology's adaptability makes it applicable to diverse prokaryotic genomic datasets.