scholarly journals Comparison of Similarity Coefficients used for Cluster Analysis with Amplified Fragment Length Polymorphism Markers in the Silkworm,Bombyx mori

2009 ◽  
Vol 9 (71) ◽  
pp. 1-8 ◽  
Author(s):  
Seyed Benyamin Dalirsefat ◽  
Andréia da Silva Meyer ◽  
Seyed Ziyaeddin Mirhoseini
Keyword(s):  
Cluster Analysis ◽  
Bombyx Mori ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Similarity Coefficients ◽  
Silkworm Bombyx Mori

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.

Amplified fragment length polymorphism analysis of different geographic populations of the gypsy moth, Lymantria dispar (Lepidoptera: Lymantriidae)

1999 ◽  
Vol 89 (1) ◽  
pp. 79-88 ◽  
Author(s):  
A. Reineke ◽  
P. Karlovsky ◽  
C.P.W. Zebitz
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Gypsy Moth ◽  
Lymantria Dispar ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Insect Pests ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Polymorphism Analysis

AbstractThe gypsy moth, Lymantria dispar Linnaeus, is one of the most serious insect pests of palaearctic and nearctic hardwood forests. We used amplified fragment length polymorphism (AFLP) to detect genetic diversity within and among gypsy moth populations. Five AFLP primer combinations were used on 98 L. dispar samples from different parts of Europe, Asia and North America, detecting a total of 481 polymorphic and 58 monomorphic fragments. Genetic similarities based on these data were calculated and cluster analysis was performed to graphically display groupings between isolates. Lymantria dispar individuals from close geographical areas of Europe were mostly grouped together in cluster analysis resulting in the formation of subgroups corresponding to the origin of the samples. Supporting this observation, clustering of individuals from 22 neighbouring populations in southern Germany agreed well with the region they originated from. Thus, AFLP analysis revealed the existence of a certain degree of genetic variability between European gypsy moth populations that could be explained by the accumulation of polymorphisms resulting from both historical population bottlenecks and the adaptation to different environmental conditions. The results of this study therefore demonstrate that AFLP analysis is a sensitive technique for distinguishing genotypes from different geographic origins as well as from neighbouring local populations and provides sufficient molecular markers for future characterization of the gypsy moth genome.

scholarly journals Genetic Relatedness of Ornamental Ficus Species and Cultivars Analyzed by Amplified Fragment Length Polymorphism Markers

2007 ◽  
Vol 132 (6) ◽  
pp. 807-815 ◽  
Author(s):  
Jinggui Fang ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Ornamental Plant ◽  
Rapid Expansion ◽  
Plant Industry ◽  
Similarity Coefficients ◽  
Woody Root

Ornamental Ficus L. is a group of lactiferous trees, shrubs, and woody root-climbing vines that are cultivated either as landscape plants in the tropics and subtropics or as foliage plants used worldwide for interiorscaping. With the recent rapid expansion of the ornamental plant industry, more new Ficus species and cultivars have been introduced. However, no study has thus far addressed the genetic relationships of cultivated ornamental Ficus. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed the genetic relatedness of 56 commercial cultivars across 12 species. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. Most cultivars were differentiated by their AFLP fingerprints, and their relationships were determined using the unweighted pair-group method of arithmetic average cluster analysis. The 56 cultivars were divided into 12 clusters that correspond to 12 species, indicating that no interspecific hybrids of ornamental Ficus are in commercial production. The 12 species are genetically diverse, with Jaccard's similarity coefficients ranging from 0.21 to 0.43. However, cultivars within three species—Ficus benjamina L., Ficus elastica Roxb. Ex Hornem., and Ficus pumila L.—are genetically close. Twenty-seven of the 29 cultivars of F. benjamina and five cultivars of F. pumila had Jaccard's similarity coefficients of 0.98 or higher respectively. Nine cultivars of F. elastica shared Jaccard's coefficients higher than 0.96. These results indicate potential genetic vulnerability of these cultivars within the three species. Because there are increasing reports of invasive pests in the ornamental plant industry, strategies for conserving genetic resources and broadening genetic diversity of cultivated Ficus are discussed.

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