A mathematical method for determining genome divergence and species delineation using AFLP

International Journal of Systematic and Evolutionary Microbiology
Christophe MougelXavier Nesme

Abstract

The delineation of bacterial species is presently achieved using direct DNA-DNA relatedness studies of whole genomes. It would be helpful to obtain the same genomically based delineation by indirect methods, provided that descriptions of individual genome composition of bacterial genomes are obtained and included in species descriptions. The amplified fragment length polymorphism (AFLP) technique could provide the necessary data if the nucleotides involved in restriction and amplification are fundamental to the description of genomic divergences. Firstly, in order to verify that AFLP analysis permits a realistic exploration of bacterial genome composition, the strong correspondence between predicted and experimental AFLP data was demonstrated using Agrobacterium strain C58 as a model system. Secondly, a method is proposed for determining current genome mispairing and evolutionary genome divergences between pairs of bacteria, based on arbitrary sampling of genomes by using AFLP. The measure of current genome mispairing was validated by comparison with DNA-DNA relatedness data, which itself correlates with base mispairing. The evolutionary genome divergence is the estimated rate of nucleotide substitution that has occurred since ...Continue Reading

Citations

May 31, 2011·Systematic and Applied Microbiology·Sabrine SaïdiRidha Mhamdi
Nov 26, 2008·Systematic and Applied Microbiology·J M Young
Sep 12, 2008·Systematic and Applied Microbiology·J M YoungE Fargier
Jun 20, 2014·Molecular Ecology·Benjamin SchulzWalter Durka
Jan 20, 2011·IEEE Transactions on Medical Imaging·Sun Y ParkUlf Gustafsson
Feb 7, 2009·International Journal of Systematic and Evolutionary Microbiology·N Ah-YouO Pruvost
Feb 12, 2015·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·F AujoulatE Jumas-Bilak
Apr 3, 2003·FEMS Microbiology Letters·Emanuele G BiondiMarco Bazzicalupo
Feb 27, 2009·FEMS Microbiology Ecology·Véronique Edel-HermannChristian Steinberg
Aug 2, 2014·PloS One·Enrique Sáez-LagunaMaría-Teresa Cervera
Jul 29, 2011·Genome Biology and Evolution·Florent LassalleXavier Nesme
Oct 22, 2008·Molecular Biology and Evolution·Denis CostechareyreXavier Nesme
Jan 31, 2013·Molecular Plant-microbe Interactions : MPMI·Vincent WalkerGilles Comte
Oct 21, 2006·Molecular Biology and Evolution·B KilianF Salamini
Nov 26, 2004·Evolution; International Journal of Organic Evolution·Kari A Segraves, Olle Pellmyr
Jun 7, 2011·Mycologia·Marie FiersChristian Steinberg
Jun 11, 2004·Genome Génome / Conseil National De Recherches Canada·F SalaminiJ Wunder
Sep 8, 2018·International Journal of Systematic and Evolutionary Microbiology·Philippe M de Lajudie, J Peter W Young
Jul 2, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Deborah Charlesworth
Jan 21, 2006·Environmental Microbiology·Hervé SanguinGeneviève L Grundmann
Oct 8, 2005·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M T CerveraW Boerjan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.