Two genetic and ecological groups of Nostoc commune in Victoria Land, Antarctica, revealed by AFLP analysis

2006 ◽  
Vol 18 (4) ◽  
pp. 573-581 ◽  
Author(s):  
Phil M. Novis ◽  
Rob D. Smissen
Keyword(s):  
Dna Sequencing ◽  
Latitudinal Gradient ◽  
Fragment Length Polymorphism ◽  
Environmental Gradients ◽  
Aflp Analysis ◽  
Ecological Groups ◽  
Nostoc Commune ◽  
Phylogeographic Pattern ◽  
Victoria Land ◽  
Intensive Sampling

Microscopy, DNA sequencing, and amplified fragment length polymorphism (AFLP) were used to examine variation within Nostoc commune from collections between 72 and 78°S in Victoria Land, Antarctica. Although there is considerable bias of collected material towards southern latitudes, and this material varies greatly in age (collected between 1984 and 2004), an important new phylogeographic pattern was found. DNA sequencing of the tRNAleu(UAA) region, used recently to define form species N. commune, revealed little variation between collections. AFLP analysis, however, split the collected material according to habitat (irrigated soil communities versus ponds), rather than latitude. These results suggest that environmental factors linked to latitude are not the greatest drivers of genetic variation in Victoria Land. These may operate at a lower level but would require intensive sampling within narrowly defined habitat types at a range of latitudes to uncover. We advocate extensive sampling across local environmental gradients based on water availability, comparative culturing, and development of sequence characterised amplified regions (SCARs) across a range of latitudes in future seasons of the Latitudinal Gradient Project.

Measuring ecosystem response in a rapidly changing environment: the Latitudinal Gradient Project

2006 ◽  
Vol 18 (4) ◽  
pp. 465-471 ◽  
Author(s):  
C. Howard-Williams ◽  
D. Peterson ◽  
W.B. Lyons ◽  
R. Cattaneo-Vietti ◽  
S. Gordon
Keyword(s):  
New Zealand ◽  
Latitudinal Gradient ◽  
Environmental Gradients ◽  
Climate Variability And Change ◽  
Victoria Land ◽  
Research Programmes ◽  
Ecosystem Studies ◽  
The Face ◽  
The Usa ◽  
Key Questions

In the face of climate variability and change, science in Antarctica needs to address increasingly complex questions. Individual small studies are being replaced by multinational and multidisciplinary research programmes. The Latitudinal Gradient Project (LGP) is one such approach that combines a series of smaller studies under a single broad hypothesis to provide information that uses a gradient in latitude as a surrogate for environmental gradients, particularly climate. In this way latitudinal differences can be used to indicate climate change differences. The Key Questions for the LGP were developed via national workshops in Italy, New Zealand, and the USA and via two international workshops at SCAR conferences. Science and logistics are currently jointly shared by New Zealand, Italy and the USA, and cover marine and inland ecosystem studies along the Victoria Land coast from 72° to 78°S with plans for extensions to 85°S. The LGP forms part of the SCAR Programme Evolution and Biodiversity in Antarctica. This Special Issue summarizes some of the work in the first three years of the LGP (2002–2005), between McMurdo Sound and Cape Hallett, to form a basis for future comparative studies as the research shifts along the latitudinal span in the next decade.

scholarly journals Genetic Diversity of Rhubarb Cultivars

2008 ◽  
Vol 133 (4) ◽  
pp. 587-592 ◽  
Author(s):  
Joseph C. Kuhl ◽  
Veronica L. DeBoer
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Length Polymorphism ◽  
Genetic Relationship ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
18Th Century ◽  
Pedigree Information ◽  
Aflp Analysis ◽  
Fingerprint Analysis

The genus Rheum L., commonly known as rhubarb, is composed of ≈60 species, primarily distributed throughout northern and central Asia. Rhubarb species have been used for medicinal purposes for thousands of years; however, it was not until the 18th century that the culinary use of petioles was first reported. Although the origin(s) of culinary rhubarb is not clear, it is thought that they originated from hybridization of rhubarb species originally brought to Europe for medicinal purposes. Most rhubarb cultivars lack pedigree information, and the genetic relationship among cultivars is largely unknown. Amplified fragment length polymorphism (AFLP) markers were generated for fingerprint analysis of 37 cultivars and four putative Rheum species accessions. Ten EcoRI and MseI primer combinations were analyzed for a total of 1400 scored polymorphisms, with an average of 140 polymorphisms per primer combination. Results show at least two clusters of related cultivars, as well as distantly related accessions. This study provides an estimate of rhubarb cultivar genetic diversity using AFLP analysis.

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.

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.

scholarly journals Relationships among Morphological Characters, Isozymes Polymorphism and DNA Variability – the Impact on Lactuca Germplasm Taxonomy

2011 ◽  
Vol 39 (No. 2) ◽  
pp. 59-67 ◽  
Author(s):  
I. Doležalová ◽  
A. Lebeda ◽  
M. Dziechciarková ◽  
E. Křístková ◽  
D. Astley ◽  
...  
Keyword(s):  
Dna Content ◽  
Fragment Length Polymorphism ◽  
Morphological Variability ◽  
Morphological Characters ◽  
Aflp Analysis ◽  
Dapi Staining ◽  
Lactuca Species ◽  
Relative Dna Content ◽  
The Impact

Fifty one accessions of nineteen Lactuca species, the hybrid L. serriola × L. sativa and the related species Mycelis muralis were evaluated for morphological variability, esterase (EST) polymorphism, Amplified Fragment Length Polymorphism (AFLP) and relative DNA content. Sixteen Lactuca accessions were classified taxonomically on the basis of morphology, isozyme analysis and AFLP. Twenty-eight bands (isoforms) of EST were recorded allowing 82% of accessions to be distinguished. The relative DNA content, measured using flow-cytometry (DAPI staining), ranged from 2.02 pg in L. capensis to 17.96 pg in L. canadensis. The results from AFLP analysis and the relative DNA content measurement corresponded well with recent taxonomic classification of the genus Lactuca.  

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

2006 ◽  
Vol 96 (10) ◽  
pp. 1097-1107 ◽  
Author(s):  
Larry J. Heilmann ◽  
Nadav Nitzan ◽  
Dennis A. Johnson ◽  
Julie S. Pasche ◽  
Curt Doetkott ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Vegetative Compatibility ◽  
Colletotrichum Coccodes ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Nit Mutants

Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

scholarly journals AFLP Analysis for Genetic Diversity in Capsicum Annuum and Related Species

2006 ◽  
Vol 1 (3) ◽  
pp. 1934578X0600100
Author(s):  
Sanjog T. Thul ◽  
Ajit K. Shasany ◽  
Mahendra P. Darokar ◽  
Suman P. S. Khanuja
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Great Degree ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Variation Analysis ◽  
Average Similarity ◽  
Geographical Locations

Intra- and inter-specific genetic variation analysis was conducted using amplified fragment length polymorphism (AFLP) profiling in Capsicum accessions in the germplasms collected from different geographical locations in India. A total of 24 accessions were investigated belonging to six species, namely C. annuum, C. baccatum, C. chinence, C. eximium, C. frutescens and C. luteum. Average similarity within the 15 accessions of C. annuum was highest (100%) between accessions CIMAP/CA45 and CIMAP/CA49 obtained from IISR, Kerala and 43% among the species CIMAP/CC1 and CIMAP/CB2. In this analysis, accessions were clustered more pronouncedly according to their geographical locations than to their taxonomic labels. A great degree of intermixing of present day domesticated chillies is evident from the present study.

Genetic analysis of mango landraces from Mexico based on molecular markers

2009 ◽  
Vol 7 (03) ◽  
pp. 244-251 ◽  
Author(s):  
Didiana Gálvez-López ◽  
Sanjuana Hernández-Delgado ◽  
Maurilio González-Paz ◽  
Enrique Noe Becerra-Leor ◽  
Miguel Salvador-Figueroa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Geographical Origin ◽  
Genetic Recombination ◽  
Genetic Relationships ◽  
Mangifera Indica ◽  
Aflp Analysis ◽  
Significant Genetic Differentiation ◽  
Simple Sequence

Genetic diversity and relationships among 112 mango (Mangifera indica) plants native to 16 states of Mexico and four controls [three mango cultivars (Ataulfo, Manila and Tommy Atkins) and one accession ofMangifera odorata] were evaluated based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Mango germplasm shows broad dispersion through Mexico and genetically similar germplasm from different agroecological regions has previously been found by our group. Both AFLP and SSR analyses indicated high genetic similarity among mango populations that were clustered in two major groups: mangos from Gulf of Mexico coastline and mangos from Pacific Ocean coastline and locations far away from the sea. The highest genetic diversity was found within plants from each state, and significant genetic differentiation (FST = 0.1921, AFLPs and 0.1911, SSRs) was also observed among mango populations based on geographical origin and genetic status (cultivars versus landraces). Heterozygosity values ranged from low (0.38) to moderate (0.68), and no heterozygote deficits were found. The highest genetic variability was found in mango populations from Tabasco, Michoacán and Oaxaca. Data suggested that mangoes are subjected to natural or induced pollination, so segregation as well as genetic recombination plays major roles on genetic diversification of Mexican mangos. AFLP analysis was more robust than SSR for determining the genetic relationships among mango landraces from Mexico.

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