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Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species

BACKGROUND: Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An import...

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Autores principales: Caballero, Armando, García-Pereira, María Jesús, Quesada, Humberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750350/
https://www.ncbi.nlm.nih.gov/pubmed/24060007
http://dx.doi.org/10.1186/1471-2164-14-528
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author Caballero, Armando
García-Pereira, María Jesús
Quesada, Humberto
author_facet Caballero, Armando
García-Pereira, María Jesús
Quesada, Humberto
author_sort Caballero, Armando
collection PubMed
description BACKGROUND: Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. RESULTS: Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1–2, and only about 50% of the genes would have markers within that distance. CONCLUSIONS: The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and detecting large islands of differentiation in the genome. However, for specific traits, the percentage of AFLP markers close to genes can be rather small. Therefore, genome scans directed towards the search of markers closely linked to selected loci can be a difficult task in many instances.
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spelling pubmed-37503502013-08-24 Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species Caballero, Armando García-Pereira, María Jesús Quesada, Humberto BMC Genomics Research Article BACKGROUND: Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. RESULTS: Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1–2, and only about 50% of the genes would have markers within that distance. CONCLUSIONS: The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and detecting large islands of differentiation in the genome. However, for specific traits, the percentage of AFLP markers close to genes can be rather small. Therefore, genome scans directed towards the search of markers closely linked to selected loci can be a difficult task in many instances. BioMed Central 2013-08-01 /pmc/articles/PMC3750350/ /pubmed/24060007 http://dx.doi.org/10.1186/1471-2164-14-528 Text en Copyright © 2013 Caballero et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Caballero, Armando
García-Pereira, María Jesús
Quesada, Humberto
Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title_full Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title_fullStr Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title_full_unstemmed Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title_short Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
title_sort genomic distribution of aflp markers relative to gene locations for different eukaryotic species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750350/
https://www.ncbi.nlm.nih.gov/pubmed/24060007
http://dx.doi.org/10.1186/1471-2164-14-528
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