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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.

Genome Copying Errors

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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.

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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

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Genomic DNA in Prokaryotes

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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.
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Although bacterial genomes are much...

Horizontal Gene Transfer

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Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...

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In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

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Published on: May 5, 2023

Toward almost closed genomes with GapFiller.

Marten Boetzer¹, Walter Pirovano

¹BaseClear BV, Leiden, The Netherlands.

|June 27, 2012

Summary

This summary is machine-generated.

GapFiller is a new automated strategy that reliably closes gaps in genome assemblies using paired reads. This bioinformatics tool significantly reduces the need for additional laboratory work to complete genome sequencing.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

De novo assembly is crucial for analyzing genomic data from next-generation sequencing.
Draft genome assemblies often contain gaps within scaffold sequences, hindering complete genome reconstruction.
Closing these gaps typically requires extensive and time-consuming wetlab validation.

Purpose of the Study:

To introduce GapFiller, an automated strategy for efficiently closing gaps in scaffold sequences.
To reduce the experimental effort required for finishing draft genome assemblies.
To provide a reliable computational tool for improving genome assembly quality.

Main Methods:

Development of an automated strategy named GapFiller.
Utilizing paired-end reads to bridge gaps within assembled scaffolds.
Testing the method on both bacterial and eukaryotic genomic datasets.

Main Results:

GapFiller successfully and reliably closed gaps in scaffold sequences.
The method demonstrated high accuracy with minimal errors across diverse datasets.
Significant reduction in the need for subsequent wetlab gap closure experiments.

Conclusions:

GapFiller offers an effective automated solution for gap closure in genome assembly.
The tool enhances the efficiency of genome sequencing projects by minimizing manual validation.
The software is publicly available, facilitating its adoption in bioinformatics research.