Amplified fragment length polymorphism analysis reveals three distinct taxa in Carex digitalis sect. Careyanae (Cyperaceae)

2006 ◽  
Vol 84 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Bruce A. Ford ◽  
Robert F.C. Naczi ◽  
Habibollah Ghazvini ◽  
Mahmood Iranpour
Keyword(s):  
North Carolina ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Additional Species ◽  
Pair Group

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis , var. floridana , var. macropoda ). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora.

Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 792-801 ◽  
Author(s):  
T Chikmawati ◽  
B Skovmand ◽  
J P Gustafson
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Aflp Data ◽  
Length Polymorphisms

Amplified fragment length polymorphism (AFLP) data were utilized to analyze the phylogenetic relationships among 29 accessions representing 14 of the most commonly recognized ranked species or subspecies in the genus Secale. We observed 789 AFLP markers of 1130 fragments utilizing 18 P-/M- and E-/M- primer combinations. All polymorphic fragments were used to construct phenetic and phylogenetic trees. The resulting phenogram and cladogram had similar tree topologies. Cluster analysis showed that Secale sylvestre was the most distantly related to all other ryes. Annual forms were grouped together, and the perennial forms appeared more closely related to each other. This suggested that life cycle could have played an important role in determining the relationships among Secale species. Secale sylvestre was considered to be the most ancient species, whereas Secale cereale was the most recently evolved species. Amplified fragment length polymorphism analysis clearly separated all Secale species into only 3 major species groups, within the genus Secale: S. sylvestre, Secale montanum (syn. Secale strictum) for perennial forms, and S. cereale for annual forms. This study demonstrated that the AFLP approach is a useful tool for discriminating species differences, and also gave a much better resolution in discerning genetic relationships among Secale species as compared with previous studies using other approaches.Key words: AFLP, Secale, phylogenetic relationship.

scholarly journals Fluorescent Amplified Fragment Length Polymorphism Analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis Isolates

2004 ◽  
Vol 70 (2) ◽  
pp. 1068-1080 ◽  
Author(s):  
Karen K. Hill ◽  
Lawrence O. Ticknor ◽  
Richard T. Okinaka ◽  
Michelle Asay ◽  
Heather Blair ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Bacillus Cereus ◽  
Bacillus Anthracis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Phenotypic Traits ◽  
Polymorphism Analysis ◽  
Aflp Data

ABSTRACT DNA from over 300 Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis isolates was analyzed by fluorescent amplified fragment length polymorphism (AFLP). B. thuringiensis and B. cereus isolates were from diverse sources and locations, including soil, clinical isolates and food products causing diarrheal and emetic outbreaks, and type strains from the American Type Culture Collection, and over 200 B. thuringiensis isolates representing 36 serovars or subspecies were from the U.S. Department of Agriculture collection. Twenty-four diverse B. anthracis isolates were also included. Phylogenetic analysis of AFLP data revealed extensive diversity within B. thuringiensis and B. cereus compared to the monomorphic nature of B. anthracis. All of the B. anthracis strains were more closely related to each other than to any other Bacillus isolate, while B. cereus and B. thuringiensis strains populated the entire tree. Ten distinct branches were defined, with many branches containing both B. cereus and B. thuringiensis isolates. A single branch contained all the B. anthracis isolates plus an unusual B. thuringiensis isolate that is pathogenic in mice. In contrast, B. thuringiensis subsp. kurstaki (ATCC 33679) and other isolates used to prepare insecticides mapped distal to the B. anthracis isolates. The interspersion of B. cereus and B. thuringiensis isolates within the phylogenetic tree suggests that phenotypic traits used to distinguish between these two species do not reflect the genomic content of the different isolates and that horizontal gene transfer plays an important role in establishing the phenotype of each of these microbes. B. thuringiensis isolates of a particular subspecies tended to cluster together.

scholarly journals High-Resolution Genotyping of Streptococcus pyogenesSerotype M1 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

1999 ◽  
Vol 37 (6) ◽  
pp. 1948-1952 ◽  
Author(s):  
Meeta Desai ◽  
Androulla Efstratiou ◽  
Robert George ◽  
John Stanley
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Geographic Origin ◽  
Amplified Fragment Length Polymorphism ◽  
Discriminatory Power ◽  
Polymorphism Analysis ◽  
Worldwide Distribution ◽  
High Discriminatory Power ◽  
Typing Methods

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise “identical” M1 isolates as members of a clone complex.

scholarly journals Genomic Relatedness of ChlamydiaIsolates Determined by Amplified Fragment Length Polymorphism Analysis

1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Genomic Relatedness

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of Escherichia coli: High-Resolution Typing Method with Phylogenetic Significance

1999 ◽  
Vol 37 (5) ◽  
pp. 1274-1279 ◽  
Author(s):  
Catherine Arnold ◽  
Lou Metherell ◽  
Geraldine Willshaw ◽  
Anthony Maggs ◽  
John Stanley
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Enzyme Electrophoresis ◽  
Typing Method ◽  
E Coli

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains ofEscherichia coli. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species E. coli, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselectiveEcoRI primer (Eco+0) and a labelled selectiveMseI primer (Mse+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of E. coli infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.

Comparative Fingerprinting Analysis ofCampylobacter jejuni subsp. jejuni Strains by Amplified-Fragment Length Polymorphism Genotyping

2000 ◽  
Vol 38 (9) ◽  
pp. 3379-3387 ◽  
Author(s):  
Bjørn-Arne Lindstedt ◽  
Even Heir ◽  
Traute Vardund ◽  
Kjetil K. Melby ◽  
Georg Kapperud
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Epidemiological Surveillance ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Ofcampylobacter Jejuni

Amplified-fragment length polymorphism (AFLP) analysis with the endonucleases BglII and MfeI was used to genotype 91 Campylobacter jejuni subsp. jejunistrains from outbreaks and sporadic cases. AFLP-generated fragments were labeled with fluorescent dye and separated by capillary electrophoresis. The software packages GeneScan and GelCompar II were used to calculate AFLP pattern similarities and to investigate phylogenetic relationships among the genotyped strains. The AFLP method was compared with two additional DNA-based typing methods, pulsed-field gel electrophoresis (PFGE) using SmaI and restriction fragment length polymorphism analysis on PCR products (PCR-RFLP) of theflaA and flaB genes. We found that AFLP analysis of C. jejuni strains is a rapid method that offers better discriminatory power than do both PFGE and PCR-RFLP. AFLP and, to a lesser extent, PCR-RFLP could differentiate strains within the same PFGE profiles, which also makes PCR-RFLP an alternative to PFGE. We were able to clearly distinguish 9 of 10 recognized outbreaks by AFLP and to identify similarities among outbreak and sporadic strains. Therefore, AFLP is suitable for epidemiological surveillance ofC. jejuni and will be an excellent tool for source identification in outbreak situations.

Sign in / Sign up

Export Citation Format

Share Document