Studies on the population structure of the Houbara BustardChlamydotis undulatain the Middle East with DNA analysis techniques

2001 ◽  
Vol 22 (1) ◽  
pp. 25-35 ◽  
Author(s):  
Marie-Ann D’Aloia
2020 ◽  
Vol 226 ◽  
pp. 105506 ◽  
Author(s):  
Isaac Wirgin ◽  
Lorraine Maceda ◽  
Matt Tozer ◽  
Joseph Stabile ◽  
John Waldman

2002 ◽  
Vol 68 (6) ◽  
pp. 2849-2857 ◽  
Author(s):  
L. Mereghetti ◽  
P. Lanotte ◽  
V. Savoye-Marczuk ◽  
N. Marquet-Van Der Mee ◽  
A. Audurier ◽  
...  

ABSTRACT To improve our understanding of the genetic links between strains originating from food and strains responsible for human diseases, we studied the genetic diversity and population structure of 130 epidemiologically unrelated Listeria monocytogenes strains. Strains were isolated from different sources and ecosystems in which the bacterium is commonly found. We used rRNA gene restriction fragment length polymorphism analysis with two endonucleases and random multiprimer DNA analysis with seven oligonucleotide primers to study multiple genetic features of each strain. We used three clustering methods to identify genetic links between individual strains and to determine the precise genetic structure of the population. The combined results confirmed that L. monocytogenes strains can be divided into two major phylogenetic divisions. The method used allowed us to demonstrate that the genetic structure and diversity of the two phylogenetic divisions differ. Division I is the most homogeneous and can easily be divided into subgroups with dissimilarity distances of less than 0.30. Each of these subgroups mainly, or exclusively, contains a single serotype (1/2b, 4b, 3b, or 4a). The serotype 4a lineage appears to form a branch that is highly divergent from the phylogenetic group containing serotypes 1/2b, 4b, and 3b. Division II contains strains of serotypes 1/2a, 1/2c, and 3a. It exhibits more genetic diversity with no peculiar clustering. The fact that division II is more heterogeneous than division I suggests that division II evolved from a common ancestor earlier than division I. A significant association was found between division I and human strains, suggesting that strains from division I are better adapted to human hosts.


2017 ◽  
Vol 16 (2) ◽  
pp. 49 ◽  
Author(s):  
Arif Wibowo ◽  
Ridwan Affandi ◽  
Kadarwan Soewardi ◽  
Sudarto Sudarto

Although the giant featherback Chitala lopis is an important fish in Kampar River, the population structure has not been investigated. In this study, genetic diversity and population structure of giant featherback were examined using nucleotide sequence analysis of mitochondrial DNA control region for 54 fish collected from Kampar River.


Plant Disease ◽  
2021 ◽  
Author(s):  
Kumarse Nazari ◽  
Emad Al-Maaroof ◽  
Ezgi Kurtulus ◽  
Handan Kavaz ◽  
Dave Hodson ◽  
...  

A wheat rust survey was conducted in Iraq in 2019 and collected 27 stem rust (caused by Puccinia graminis Pers.:Pers. f. sp. tritici Erikks. & E. Henn.) samples. Seven samples were viable, and they were tested for races of P. graminis f. sp. tritici at the Regional Cereal Rust Research Center (RCRRC) in Izmir, Turkey under strict quarantine procedures. Two 0.5 cm segments of each infected stem sheath were incubated in a petri dish at 20°C for three hours for re-hydration of urediniospores, which were multiplied on 10-day old seedlings of susceptible cultivar Morocco grown in a spore free growth chamber at 18°C and 16 hours light. Inoculated seedlings underwent a dew period at 18°C for 16 hours dark and 8 hours fluorescent light and 95% relative humidity. Three days after moving the pots to a growth chamber with eight hours dark at 18°C and 16 hours light (300 µmol m-2s-1), each pot was covered using a cellophane bag. Bulk urediniospores of each collection were collected 14 days post-inoculation from a cellophane bag using a mini cyclone spore collector connected to a gelatin capsule. One ml of 3M Novec™ oil was added to each capsule, and spores were inoculated onto 20 North American stem rust differential lines using the standard procedures (Jin et al. 2008). Pre-inoculation, inoculation, incubation, and post-inoculation conditions were the same as above. Seedling infection types (ITs) were recorded 14 days post-inoculation using 0 to 4 scale (Stakman et al. 1962). Race designation followed the five- letter code nomenclature described by Jin et al. (2008). Out of the seven samples, four were typed as TKKTF, two as TKTTF, and one collected from an advanced breeding bread wheat line “Shahoo 2” (Inqalab 91*2/Tukuru) in a trial site at Halabja governorate showed mixed ITs of 11+ and 3+ for lines carrying Sr11, Sr24, Sr36, and Sr31. Three single pustule (SP) isolates were developed from the IT of 3+ pustules collected from the Sr31 tester line, and one SP isolate was developed from the IT 11+ pustule collected from the Sr11 source. After spore multiplication, the SP-derived isolates were inoculated on the 20 North American differential lines. To confirm virulence/avirulence on Sr24, Sr31, and Sr36, cultivars Siouxland (PI 483469, Sr24+Sr31) and Sisson (PI 617053, Sr36+Sr31) were also inoculated. All seedling assays were repeated three times. The three SP isolates virulent on Sr31 were designated as race TTKTT, and the SP isolate virulent on Sr11 was designated as TKTTF. Seedling ITs of 3+ and 0; were recorded for Siouxland and Sisson against TTKTT, respectively, and both cultivars showed IT of 1+ against TKTTF. Race TKTTF was similar to TKKTF except for additional virulence on Sr36, and TTKTT differed from the other two races being virulent on Sr24 and Sr31. DNA analysis of three TTKTT isolates from Kenya and the TTKTT isolate from Iraq using a diagnostic qPCR assay developed by the USDA-ARS Cereals Disease Laboratory (Ug99 RG stage 1, Szabo unpublished) confirmed that all tested isolates belonged to the Ug99 lineage. Race TTKTT was first reported from Kenya in 2014 (Patpour et al. 2016), and in 2018 from Ethiopia (Hei et al. 2020). We report the first detection of TTKTT in Iraq and the Middle East region. This represents only the third instance of a member of the Ug99 race group outside of Africa since first detection of race TTKSK in Yemen in 2006, and Iran in 2007 (Nazari et al. 2009). The continued spread of stem rust races with complex virulence and the increasing frequency and early onset of stem rust infections in the Middle East is a cause for concern. Continuous support for rust surveillance and race typing in this region remains crucial. References: Hei, N. B., et al. 2020. Plant Dis. 104:982. Jin, Y., et al. 2008. Plant Dis. 92:923-926. Nazari, K., et al. 2009. Plant Dis. 93:317. Patpour, M., et al. 2016. Plant Dis. 100:522. Stakman, E. C., et al. 1962. Identification of physiological races of Puccinia graminis var. tritici. U. S. Dep. Agric. ARS E-617.


2020 ◽  
Vol 10 (3) ◽  
pp. 1064 ◽  
Author(s):  
Hye-Ji Oh ◽  
Paul Henning Krogh ◽  
Hyun-Gi Jeong ◽  
Gea-Jae Joo ◽  
Ihn-Sil Kwak ◽  
...  

We designed an experiment to analyze the gut content of Rotifera based on DNA barcoding and tested it on Asplanchna sp. in order to ensure that the DNA extracted from the rotifer species is from the food sources within the gut. We selected ethanol fixation (60%) to minimize the inflow effects of treated chemicals, and commercial bleach (the final concentration of 2.5%, for 210 s) to eliminate the extracellular DNA without damage to the lorica. Rotifers have different lorica structures and thicknesses. Therefore, we chose a pretreatment method based on Asplanchna sp., which is known to have weak durability. When we used the determined method on a reservoir water sample, we confirmed that the DNA fragments of Chlorophyceae, Diatomea, Cyanobacteria, and Ciliophora were removed. Given this result, Diatomea and cyanobacteria, detected from Asplanchna, can be considered as gut contents. However, bacteria were not removed by bleach, thus there was still insufficient information. Since the results of applying commercial bleach to rotifer species confirmed that pretreatment worked effectively for some species of rotifers food sources, in further studies, it is believed to be applicable to the gut contents analysis of more diverse rotifers species and better DNA analysis techniques by supplementing more rigorous limitations.


Conventional DNA analysis techniques include cleavage of DNA by restriction enzymes, fragment electrophoresis, Southern transfer, probe labeling, probegenomic fragment hybridization, and print detection (Cawood 1989, Sambrook 1989, Berger 1987). Details of the assay conditions may vary considerably depending on the specific probes hybridized. Endonuclease digestion, electrophoresis, and Southern transfer are not required with simple dot-blot procedures. The quality of the final result can be no greater than the quality of the input DNA specimen and the attention of the analyst to assay details. The format of the analysis blot must be carefully considered to include control specimens and a broad range of size markers. The analyst must also be certain about the sizes of the profile fragments to accurately determine if matches exist between crime evidence and suspect specimen or offspring and putative parent specimens and to calculate the match probabilities. Restriction enzymes cleave DNA at specific recognition base sequences. It is important to choose an enzyme with sites flanking the repeats when fragments consisting of different numbers of tandem repeats are to be characterized for DNA profiling. Cleavage within a repeat sequence will result in the production of small fragments that may be unresolvable. The choice of enzyme, in this respect, is accomplished either by trial and error or by knowledge of the base sequence of the fragment flanking regions. The optimum reaction conditions vary for each enzyme; consequently, suppliers usually provide information sheets for the user. Digestion temperature and buffer salt concentration are the critical features. The reaction mixture can be overlaid with a few drops of paraffin oil to prevent vapor formation and changes in the buffer concentration. This applies mainly to enzymes such as Taq I that require high reaction temperatures (65°C in this example). Unless specifically indicated otherwise, three different strength ionic buffers will accommodate most enzymes.


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