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Gene Flow

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Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.

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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.

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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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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...

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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...

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ConSpeciFix: classifying prokaryotic species based on gene flow.

Louis-Marie Bobay¹, Brian Shin-Hua Ellis², Howard Ochman²

¹Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA.

Bioinformatics (Oxford, England)

|May 18, 2018

Summary

This summary is machine-generated.

ConSpeciFix offers a new method for classifying prokaryotic species based on the Biological Species Concept, moving beyond simple sequence similarity. This approach provides a more biologically relevant foundation for defining species across all domains of life.

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Area of Science:

Microbiology
Bioinformatics
Evolutionary Biology

Background:

Current prokaryotic species classification relies on sequence similarity thresholds, which lack a strong biological basis.
This method can lead to inconsistencies and a lack of biological relevance in species definitions.

Purpose of the Study:

To introduce ConSpeciFix, a novel computational tool for prokaryotic species classification.
To implement the Biological Species Concept for a more biologically grounded approach to prokaryotic taxonomy.

Main Methods:

ConSpeciFix utilizes criteria from the Biological Species Concept for species delineation.
The program integrates established bioinformatics tools such as Usearch, MCL, MAFFT, and RAxML.

Main Results:

ConSpeciFix provides a unified framework for species definition across all domains of life.
The program offers a more biologically relevant alternative to traditional sequence similarity-based methods.

Conclusions:

ConSpeciFix represents a significant advancement in prokaryotic taxonomy.
This tool promotes a consistent and biologically meaningful approach to defining prokaryotic species.