The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes.
نویسندگان
چکیده
The amplified fragment length polymorphism (AFLP) technique is being increasingly used in phylogenetic studies, especially in groups of rapidly radiating taxa. One of the key issues in the phylogenetic suitability of this technique is whether the DNA fragments generated via the AFLP method are homologous within and among the taxa being studied. We used a bioinformatics approach to assess homology based on both chromosomal location and sequence similarity of AFLP fragments. The AFLP technique was electronically simulated on genomes from eight organisms that represented a range of genome sizes. The results demonstrated that within a genome, the number of fragments is positively associated with genome size, and the degree of homology decreases with increasing numbers of fragments generated. The average homology of fragments was 89% for small genomes (< 400 Mb) but decreased to 59% for large genomes (> 2 Gb). Fragment homology for large genomes can be increased by excluding smaller fragments, although there is no clear upper limit for the size of fragments to exclude. A second approach is to increase the number of selective nucleotides in the final selective amplification step. For strains of the same organism, homology based on chromosome location and sequence similarity of fragments was 100%. Fragment homology for more distantly related taxa, however, decreased with greater time since divergence. We conclude that AFLP data are best suited for examining phylogeographic patterns within species and among very recently diverged species.
منابع مشابه
Genetic Variability in Growth Hormone Gene and Association between Restriction Fragment Length Polymorphisms (RFLP) Patterns and Quantitative Variation of Live Weight, Carcass, Behaviour, Heterophil and Lymphocyte Traits in Japanese Quails
Growth hormone gene plays a critical role in regulating growth and metabolism which leads to potential correlations between the polymorphisms of this gene and economic trait. A 776 bp fragment within the intron 1 region of the growth hormone gene from 346 individuals of an F2 population of Japanese quail was amplified. The polymerase chain reaction (PCR) product was digested using MspI restrict...
متن کاملComparison of Genetic Diversity in Species and Cultivars of Pistachio (Pistacia sp. L.) Based on Amplified Fragment Length Polymorphism (AFLP) Markers
The genetic diversity of a large number of pistachio genotypes grown in Iran is not exactly known. Most of the studies on genetic diversity of Iranian pistachio varieties are based on morphological characteristics or isozyme markers. In the present study, the genetic diversity of selected pistachio cultivars along with some wild species were evaluated by Amplified Fragment Length Polymorphism (...
متن کاملAnalysis of the Genetic Diversity 12 Iranian Damask Rose (Rosa damascena Mill.) Genotypes Using Amplified Fragment Length Polymorphism Markers
In this study, the genetic diversity of 12 Iranian Damask rose (Rosa damascena Mill.) genotypes was studied using amplified fragment length polymorphism (AFLP) markers. Twelve AFLP primer combinations generated 483 polymorphic bands and showed extreme variability and genetic complexity among the studied genotypes. The AFLP analysis revealed a specific amplified fragment for the genotypes collec...
متن کاملNovel Single Nucleotide Polymorphisms (SNPs) in Two Oogenesis Specific Genes (BMP15, GDF9) and Their Association with Litter Size in Markhoz Goat (Iranian Angora)
BMP15 and GDF9 are two oogenesis specific genes play a pivotal role in female fertility in mammals and potential for improvement of prolificacy in marker-assisted selection. The aim of present research was to investigate the variation and association between BMP15 and GDF9 polymorphism and litter size in Markhoz goats. The sequence variability of the different amplified fragments utilized for g...
متن کاملGenetic relationships among collections of the Persian sturgeon, Acipenser percicus, in the south Caspian Sea detected by mitochondrial DNA Restriction fragment length polymorphisms
In the present study, mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used to assess the population structure and genetic relationships among six Persian sturgeon, Acipenser persicus populations from south Caspian Sea along the Iranian coast. The complete nucleotide dehydrogenase subunit 5 (NADH 5) region of mtDNA amplified by PCR was di...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Systematic biology
دوره 56 3 شماره
صفحات -
تاریخ انتشار 2007