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 (H avp = 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.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Sporothrix (Ophiostomatales) comprises species that are pathogenic to humans and other mammals as well as environmental fungi. Developments in molecular phylogeny have changed our perceptions about ...the epidemiology, host-association, and virulence of Sporothrix. The classical agent of sporotrichosis, Sporothrix schenckii, now comprises several species nested in a clinical clade with S. brasiliensis, S. globosa, and S. luriei. To gain a more precise view of outbreaks dynamics, structure, and origin of genetic variation within and among populations of Sporothrix, we applied three sets of discriminatory AFLP markers (#3 EcoRI-GA/MseI-TT, #5 EcoRI-GA/MseI-AG, and #6 EcoRI-TA/MseI-AA) and mating-type analysis to a large collection of human, animal and environmental isolates spanning the major endemic areas. A total of 451 polymorphic loci were amplified in vitro from 188 samples, and revealed high polymorphism information content (PIC = 0.1765–0.2253), marker index (MI = 0.0001–0.0002), effective multiplex ratio (E = 15.1720–23.5591), resolving power (Rp = 26.1075–40.2795), discriminating power (D = 0.9766–0.9879), expected heterozygosity (H = 0.1957–0.2588), and mean heterozygosity (Havp = 0.000007–0.000009), demonstrating the effectiveness of AFLP markers to speciate Sporothrix. Analysis using the program structure indicated three genetic clusters matching S. brasiliensis (population 1), S. schenckii (population 2), and S. globosa (population 3), with the presence of patterns of admixture amongst all populations. AMOVA revealed highly structured clusters (PhiPT = 0.458–0.484, P < 0.0001), with roughly equivalent genetic variability within (46–48 %) and between (52–54 %) populations. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for S. schenckii (χ2 = 2.522; P = 0.1122), supporting random mating. In contrast, skewed distributions were found for S. globosa (χ2 = 9.529; P = 0.0020) with a predominance of MAT1-1 isolates, and regional differences were highlighted for S. brasiliensis with the overwhelming occurrence of MAT1-2 in Rio de Janeiro (χ2 = 14.222; P = 0.0002) and Pernambuco (χ2 = 7.364; P = 0.0067), in comparison to a higher prevalence of MAT1-1 in the Rio Grande do Sul (χ2 = 7.364; P = 0.0067). Epidemiological trends reveal the geographic expansion of cat-transmitted sporotrichosis due to S. brasiliensis via founder effect. These data support Rio de Janeiro as the centre of origin that has led to the spread of this disease to other regions in Brazil. Our ability to reconstruct the source, spread, and evolution of the ongoing outbreaks from molecular data provides high-quality information for decision-making aimed at mitigating the progression of the disease. Other uses include surveillance, rapid diagnosis, case connectivity, and guiding access to appropriate antifungal treatment.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
• Biosynthesis of the sesquiterpene lactone and potent antimalarial drug artemisinin occurs in glandular trichomes of Artemisia annua plants and is subjected to a strict network of developmental and ...other regulatory cues. • The effects of three hormones, jasmonate, gibberellin and cytokinin, were studied at the structural and molecular levels in two different A. annua chemotypes by microscopic analysis of gland development, and by targeted metabolite and transcript profiling. Furthermore, a genome-wide cDNA-amplified fragment length polymorphism (AFLP)-based transcriptome profiling was carried out of jasmonate-elicited leaves at different developmental stages. • Although cytokinin and gibberellin positively affected at least one aspect of gland formation, these two hormones did not stimulate artemisinin biosynthesis. Only jasmonate simultaneously promoted gland formation and coordinated transcriptional activation of biosynthetic gene expression, which ultimately led to increased sesquiterpenoid accumulation with chemotype-dependent effects on the distinct pathway branches. Transcriptome profiling revealed a trichome-specific fatty acyl- coenzyme A reductase, trichome-specific fatty acyl-CoA reductase 1 (TFAR1), the expression of which correlates with trichome development and sesquiterpenoid biosynthesis. • TFAR1 is potentially involved in cuticular wax formation during glandular trichome expansion in leaves and flowers of A. annua plants. Analysis of phytohormone-modulated transcriptional regulons provides clues to dissect the concerted regulation of metabolism and development of plant trichomes.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Penstemon bicolor is a relatively rare, short-lived perennial herb of conservation concern and is found in the Mojave Desert and surrounding areas of southern Nevada, southeastern California, and ...northwestern Arizona. Two varieties of P. bicolor are named according to the color of their corolla: variety bicolor, the yellow or pink-colored form, and variety roseus, the magenta-colored form. The rarity of P. bicolor var. bicolor, coupled with its limited distribution, raises concerns about the genetic diversity present in the species, which is critical for the survival of species in the face of environmental stressors, such as habitat loss. Conservation management strategies for P. bicolor rely partially on the taxonomic status of variety bicolor and variety roseus; if these varieties are in fact distinct genetic lineages more appropriately defined as different species, then the implementation and urgency of management strategies would require updating accordingly. We analyzed amplified fragment length polymorphisms and inter-simple sequence repeats for 13 populations of P. bicolor from southern Nevada and northwestern Arizona to assess genetic diversity within the species and to identify the genetic distinctiveness, if any, between varieties. Our findings reveal surprisingly high levels of genetic diversity, in contrast to expectations for rare, perennial, outcrossing plants. Penstemon bicolor does, however, face ongoing threats of habitat destruction and potential local extirpation due to urbanization of the greater Las Vegas area, and we recommend that the current protective status of the species be maintained. Additionally, our analyses of differentiation failed to reveal genetic distinctiveness between varieties; we thus do not recommend that varieties of P. bicolor be elevated to species level.
Full text
Available for:
BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
•AFLP analysis and ploidy were used to evaluate 132 accessions of Aronia.•Aronia was found to be comprised of four, or possibly five, species and seven taxonomic groups.•arbutifolia was tetraploid, ...and A. prunifolia was typically tetraploid, and rarely triploid.•Diploid A. melanocarpa were found in New England, but elsewhere they were tetraploid.•Formation of A. prunifolia as a hybrid of A. arbutifolia by A. melanocarpa is supported by AFLP analysis and ploidy.
Speciation in Aronia is complex based on Amplified Fragment Length Polymorphism (AFLP) and ploidy analysis of 132, mostly wild, accessions. There are four species of Aronia and seven taxonomic groups comprised of species by ploidy combinations. A. melanocarpa can be diploid or tetraploid, with diploid forms occurring in New England and tetraploid forms occurring primarily outside of New England. A. arbutifolia was only found as a tetraploid and did not appear to occur throughout parts of New England as is generally accepted. It is likely that numerous misidentifications of A. arbutifolia have occurred historically. Almost all wild A. prunifolia were tetraploid, with the exception of a single triploid plant. Evidence from AFLP analysis and several accessions expressing a continuum of morphological characteristics between those of A. arbutifolia and A. melanocarpa suggest that A. prunifolia is of interspecific hybrid origin. The occurrence of a natural triploid A. prunifolia accession and our ability to easily create triploid A. prunifolia progeny from diploid A. melanocarpa by tetraploid A. arbutifolia crosses supports the hybrid formation of the A. prunifolia species. Hybrid A. prunifolia origin is also supported by the prevalence of A. prunifolia accessions in geographic areas where A. arbutifolia and diploid A. melanocarpa interface. Most likely, tetraploid A. prunifolia found in the wild result from repeated formation of triploid F1 interspecific hybrids and the triploid bridge mechanism. AFLP analysis, along with morphology and phenology, suggest that a new species of black-fruited Aronia (melanocarpaS) exists in the southern part of the A. melanocarpa geographic range. A. melanocarpaS plants are placed on a separate branch of the AFLP dendrogram that is separate from other Aronia species. Several accessions with large, wide leaves, large fruits and non-rhizomatous growth were found to be A. mitschurinii, an intergeneric hybrid between Aronia and Sorbus. All A. mitschurinii accessions were tetraploid.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies ...coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).
AFLP fingerprinting of the 98 main sweetpotato varieties planted in China has been constructed. Using 17 AFLP primer combinations which were selected from 1 208 primer combinations and generated the ...most amounts of polymorphic bands, AFLP analysis of the 98 main sweetpotato varieties gave a total of 410 clear polymorphic bands with an average of 24.12 polymorphic bands per primer combination. Each one of the 98 sweetpotato varieties could be clearly distinguished by EcoR I-cta/Mse I-ggc primer combination which generated the most polymorphic bands. AFLP-based genetic distance ranged from 0.0546 to 0.5709 with an average of 0.3799. The dendrogram based on AFLP markers indicated that sweetpotato varieties coming from the same regions or having same parents were clustered in the same groups. Analysis of molecular variance （AMOVA） revealed greater variations within regions （94.08%） than among regions （5.92%）. Thus, the genetic variations mainly existed within regions, while the variations among regions were very low in the tested sweetpotato varieties. Significant genetic variations existed between ＂Northern＂ and ＂Southern＂ sweetpotato varieties when Yangtze River was used as the dividing line.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to ...divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.
The genetic and epigenetic diversity, structure, and differentiation of 10 Scabiosa columbaria populations were explored in both the field and a common garden. Genetic and epigenetic variation was subsequently correlated with trait variation that was measured in both field and common garden plants. By comparing epigenetic variation in both the field and common environment, our study provides important insights into the environmental and genetic components of epigenetic variation.
Full text
Available for:
FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Jatropha curcas L. (Euphorbiaceae) has gained considerable importance as a renewable source of energy. Various molecular markers were employed to explore the genetic diversity in J. curcas germplasm. ...In present study, methylation-sensitive AFLP (MS-AFLP) markers were evaluated to analyze the divergence among five elite germplasm (CSMCRI-1 to 5) of J. curcas and subsequently the results were compared with that of AFLP markers to assess the potential utility of MS-AFLP markers for phylogenetic characterization. Study compared the genetic (obtained through AFLP marker) polymorphism with that of epigenetic (obtained through MS-AFLP marker) polymorphism. Among the germplasms studied, 07 selective combinations of MS-AFLP primers produced 40 epigenetic (methylation) polymorphic markers, while 17 AFLP primers produced 105 genetic polymorphic markers. MS-AFLP analysis showed 44.44% epigenetic polymorphism while AFLP showed 15.20% genetic polymorphism. Epigenetic and genetic polymorphism among the germplasms ranged from 12.50% to 66.67% and 2.27% to 48.57% respectively. Highest mean epigenetic polymorphism was recorded in CSMCRI-3, while highest mean genetic polymorphism was recorded in CSMCRI-1. Results showed that the genetic and epigenetic structures of J. curcas were not same and epigenetic variations are greater than the genetic variations. Differences in DNA methylation and polymorphism among the studied genotypes under prevailing environment indicate evolution of genetic and epigenetic components in different directions. The study paves idea that genotypes exhibiting less genetic divergence might possess high epigenetic divergence and this along with genetic background could be a base for selection of elite cultivar adapted to particular geo-climatic conditions for further breeding program.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity ...diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
Full text
Available for:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
PDF
