Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the ...P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67–87 fragments), the values of polymorphism information content (PIC = 0.3345–0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788–60.3818), resolving power (Rp = 22.3152–34.3152), discriminating power (D = 0.5183–0.5553), expected heterozygosity (H = 0.4247–0.4443), and mean heterozygosity (Havp = 0.00002–0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651–0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (χ2 = 1.025; P = 0.3113), P. venezuelensis (χ2 = 0.692; P = 0.4054), and P. lutzii (χ2 = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (χ2 = 8.909; P = 0.0028) and P. restrepiensis (χ2 = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of Paracoccidioides species, guiding disease-control strategies to mitigate PCM.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•Sixty pecan accessions were morphologically, chemically and genetically evaluated.•Morphometric measures presented mean values similar to estimations previously reported.•Chemical composition is ...near homogeneous among accessions.•Genetic splitting of accessions was not related to other traits, but revealed high diversity.•The retrieved data have suitable application for species breeding and the release of new cultivars.
Pecan (Carya illinoinensis) is an important commercially cultivated nut tree grown in several countries around the world, including temperate, tropical and subtropical regions. We employed morphometric, chemical and genetic analyses to characterize 60 pecan accessions from Southern Brazil. Here we show that a large spectrum of morphological traits is conserved in the trees cultivated by local farmers. On the other hand, chemical composition of the accessions did not diverge significantly. In addition, moderate to high genetic diversity is observed in these plants. Based on these results, we suggest the use of Participatory Plant Breeding as strategy for conservation of the genetic resources of pecan and improvement of nut production and commercialization. Moreover, the intellectual property of the farmers responsible for the genetic improvement of pecan have to be recognized and protected, since it is the key factor in this process.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Researchers in the field of molecular ecology and evolution require versatile and low‐cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago ...and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start‐up time before data can be generated is often less than a week. Built‐in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA‐AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
is a globally emerging multidrug resistant fungal pathogen causing nosocomial transmission. We report an ongoing outbreak of
in a London cardio-thoracic center between April 2015 and July 2016. This ...is the first report of
in Europe and the largest outbreak so far. We describe the identification, investigation and implementation of control measures.
Data on
case demographics, environmental screening, implementation of infection prevention/control measures, and antifungal susceptibility of patient isolates were prospectively recorded then analysed retrospectively. Speciation of
is was performed by MALDI-TOF and typing of outbreak isolates performed by amplified fragment length polymorphism (AFLP).
This report describes an ongoing outbreak of 50
cases over the first 16 month (April 2015 to July 2016) within a single Hospital Trust in London. A total of 44 % (
= 22/50) patients developed possible or proven
infection with a candidaemia rate of 18 % (
= 9/50). Environmental sampling showed persistent presence of the yeast around bed space areas. Implementation of strict infection and prevention control measures included: isolation of cases and their contacts, wearing of personal protective clothing by health care workers, screening of patients on affected wards, skin decontamination with chlorhexidine, environmental cleaning with chorine based reagents and hydrogen peroxide vapour. Genotyping with AFLP demonstrated that
isolates from the same geographic region clustered.
This ongoing outbreak with genotypically closely related
highlights the importance of appropriate species identification and rapid detection of cases in order to contain hospital acquired transmission.
Hybridization and introgression have a significant impact on the taxonomically controversial genus Pulmonaria. Within this genus, the P. hirta complex shows puzzling systematic relationships among ...P. hirta s.str. (2n = 22, 26 28), P. apennina (2n = 22 26), and P. vallarsae (2n = 22), showing range overlaps and mixed phenotypes in southern Europe. We carried out morphometric analyses of basal leaves and flower features along with AFLP characterization of 236 plants belonging to 11 populations within the complex and 1 population of P. officinalis. We also implemented an already available phylogeny with sequences from our target populations and characterized their karyotype. For all the populations within the complex, we found molecular evidence of a hybrid origin involving species belonging to different clades (angustifolia and officinalis clades). However, there is a certain morphological differentiation between some populations (“hirtoid” morph) and others (“vallarsoid” morph), albeit single individuals or entire populations show intermediate features. According to our results, hybridization and/or backcrossing/introgression have occurred, and gene flow is currently taking place among these “taxa”. Following the hybridization event(s), we can elaborate three possible evolutionary scenarios: (1) one hybrid “vallarsoid” (2n = 22) species spread across the Italian peninsula, and from this originated the “hirtoid” morph (2n = 28) through dysploidy; (2) two geographically distinct hybridization events produced both “vallarsoid” and “hirtoid” morphs; (3) one “hirtoid” alloploid hybrid species originated and backcrossed with P. officinalis generating “vallarsoid” plants. Under scenarios 1 and 2, the different morphs met again in central Italy, with massive current gene flow. Under scenario 3, “vallarsoid” plants spread across the Italian peninsula, but further backcrossed with “hirtoid” plants in central Italy, leaving pure lineages of “vallarsoid” plants only in the extreme north and south of their range. This latter scenario is supported by populations with 2n = 22, 26 chromosomes, having karyotype asymmetry indices intermediate between those of 2n = 16 and 2n = 28 cytotypes. Irrespective of the evolutionary dynamics, today, a single lineage showing three cytotypes occurs throughout the Italian peninsula, supporting the circumscription of a single polymorphic species, namely P. hirta.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
27.
Molecular Epidemiology of Fonsecaea Species Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A. ...
Emerging infectious diseases,
03/2011, Volume:
17, Issue:
3
Journal Article
Peer reviewed
Open access
To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology ...and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
تمّت دراسة القرابة الوراثية بين27 طرازًا وراثيًا من نبات دوّار الشمس Helianthus annuus، باستخدام139 مؤشّرًا جزيئيًا من نوع AFLP. تراوحت نسبة المؤشرات الجزيئية المتباينة بين 19.23% لدى المرئسة E41M61 ...و36.84% لدى المرئسة E35M59، في حين كانت قيم PIC متقاربة جدًا بين المرئسات بمعدّل قدره 0.37. أعطى تحليل التشابه باستخدام المؤشرات المتباينة والمتماثلة معًا قيمًا عالية تراوحت من 0.797 بين الطرازين الوراثيين 441 وHysum33 إلى 0.985 بين الطرازين غاب4 وغاب5، أمّا المؤشرات المتباينة فقط فقد استطاعت إبراز الاختلافات الوراثية بشكل أوضح؛ إذ انخفضت قيم التشابه إلى 0.156 بين الطرازين 441 وHysum33. أظهرت شجرة القرابة التي أنشئت على أساس مجموعات الأزواج ودليل Jaccard بعض التجمّعات أهمّها عنقود طرز الغاب الذي ضمّ أيضا طرازين حلبيين (مضخ حلب وسفيرة حلب)، مما يشير إلى احتمال وجود أب مشترك انحدرت منه هذه الطرز. أظهرت النتائج تنوّعًا وراثيًا هامًا بين الطرز المدروسة، كما أنّها اقترحت على أساس جزيئي أفضل الآباء من أجل برامج التحسين الوراثي المستقبلية.
Chromochloris zofingiensis
(Dönz) Fucíková & L.A.Lewis, due to its production of highly valuable carotenoids such as astaxanthin, is a model organism in biotechnology. Since the recognition of this ...physiological property, many biotechnological applications have only used a single strain (SAG 211-14 = CCAP 211/14 = UTEX 32 = ATCC 30412) to produce biomass and carotenoids. However, multiple acquisitions of strains putatively belonging to the same species raised the question of the conspecificity of those strains and their properties. In this study, the conspecificity of the available strains, which are deposited axenically in SAG, was tested using SSU and ITS rDNA sequencing and AFLP (
Eco
RI/
Pst
I) analyses. The comparison of SSU and ITS rDNA sequences as well as the AFLP patterns revealed that the investigated strains formed two very similar groups, (1) SAG 211-14, SAG 4.80, SAG 31.80, and SAG 34.80 and (2) SAG 221-2. All strains belonged to one species,
C. zofingiensis
, and represented one monophyletic lineage within the so-called DO-group of the Chlorophyceae. The robustness to cryopreservation and the subsequent epigenetic variability was detected using the methylation-sensitive AFLP (
Eco
RI/
Msp
I and
Eco
RI/
Hpa
II) among the five
Chromochloris
strains. All strains showed a high rate of survival (54.4–98.1%) during cryopreservation. The methylation patterns varied between precryo and postcryo in all strains detected among three time points (before, shortly after, and 8 weeks after cryopreservation), showing that the MS-AFLP technique has the potential to detect epigenetic effects occurring in response to cryopreservation and other stresses. Finally, the potential of these five strains for usage in biotechnological applications was proven by growing them in aerated cultures with and without additional carbon dioxide supply. The comparison showed that all strains produced high amounts of biomass and carotenoids under aeration with additional CO
2
and were therefore suitable in biotechnology.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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