Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Ustilago hordei Causing Covered Smut of Barley

Kashyap, Prem Lal; Kumar, Sudheer; Kumar, Ravi; Tripathi, Rahul; Sharma, Palika; Sharma, Anju; Jasrotia, Poonam; Singh, Gyanendra Pratap

doi:10.3389/fmicb.2019.02929

Cited by 9 publications

(7 citation statements)

References 46 publications

(60 reference statements)

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“…The AMOVA showed relatively high proportion of variability explained by the division of T rubrum sample into ST1 and ST2 groups, 22%‐48% depending on the distance metrics. It was not less than in other studies on clonal filamentous ascomycetes with 19%‐21% of variability between intraspecific groups 46,47 or filamentous ascomycetes with mixed reproduction mode, with 2%‐13% of total variability explained by differences between intraspecific groups 48,49 …”

Section: Discussionmentioning

confidence: 54%

“…16 46,47 or filamentous ascomycetes with mixed reproduction mode, with 2%-13% of total variability explained by differences between intraspecific groups. 48,49 Intraspecific genetic lines in fungi sometimes demonstrate restricted geographic ranges. [50][51][52][53] Here, we compiled the map of global distribution of T rubrum genetic lineages (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

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Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Pchelin

Mochalov

Azarov

et al. 2020

Mycoses

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Trichophyton rubrum is an ascomycete from the order Onygenales. It is prevalent fungus of medical importance in most countries due to its major contribution to the aetiology of toenail onychomycosis and foot skin mycosis. 1 Trichophyton rubrum sensu stricto is a part of species group, which also includes T violaceum and T soudanense along with several forms, potentially deserving species status. All of these can be differentiated by ribosomal DNA internal transcribed spacer (ITS) region sequences. 2-6 Statistical analysis of genetic

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Pchelin

Mochalov

Azarov

et al. 2020

Mycoses

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“…Thus, domestication, introduction, and continuous cultivation of host plants of B. sorokiniana could be the plausible explanation for topical population expansion in different wheat growing zones of India. Such type of fungal population movement has been documented in different types of fungal pathogens (Kashyap et al 2020b;Dietzel et al 2019;Katoch et al 2016;Linde et al 2010;Zaffarano et al 2008).…”

Section: Discussionmentioning

confidence: 93%

Molecular Diversity, Haplotype Distribution and Gene Flow of Bipolaris Sorokiniana Fungus Causing Spot Blotch Disease in Different Wheat Growing Zones

Kashyap¹,

Kumar²,

Sharma³

et al. 2021

Preprint

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Bipolaris sorokiniana (BS) is an economically important fungal pathogen causing spot blotch of wheat (Trtiticum aestivum) and found in all wheat growing zones of India. Very scanty and fragmentary information is available on its genetic diversity. The current research is the first detailed report on the geographic distribution and evolution of BS population in five geographically distinct wheat growing zones [North Western Plain Zone (NWPZ), North Eastern Plain zone (NEPZ); North Hill Zone (NHZ), Southern Hill Zone (SHZ) and Peninsular Zone (PZ)] of India, studied by performing nucleotide sequence comparison of internal transcribed spacer region of 183 isolates. A moderate to high levels of haplotypic diversity was noticed in different wheat growing zones. Phylogenetic analysis suggests that B. sorokiniana exist in two distinct lineages as all isolates under study were grouped in two different clades and found analogous to the findings of haplotypic and median joining network analysis. The genetic parameters revealed the existence of 59 haplotypes with three major haplotypes (H_2, H_3, and H_25) which showed star-like structure network surrounded by several single haplotypes, revealing high frequency of the mutations ((Eta = 2 – 437) in total analyzed population. H_3 was observed as a predominant haplotype and prevalent in all the five zones. Moderate level of genetic differentiation was found between NEPZ and PZ (Fst = 0.563), whereas it was low between NEPZ and NHZ (Fst = -0.062). High level of gene flow was noticed between NWPZ and NEPZ (Nm = 14.32), while it was found minimum between SZ and NHZ (Nm = 0.50). Moreover, negative score of neutrality statistics (Tajima’s D and Fu’s FS test) for NWPZ, PZ and SHZ populations, suggested recent population expansion in these zones. However, positive score for both the neutrality tests observed in NEPZ and NHZ indicated the dominance of balancing selection in structuring their population. Recombination events were observed in the NWPZ, NEPZ and NHZ population, while it was absent in SHZ and PZ population. Thus, the lack of any specific genetic population structure in all the zones indicates for the expansion history only from one common source population i.e. NWPZ, a mega zone of wheat production in India. Overall, it seems that the predominance of individual haplotypes with a moderate level of genetic variation and men mediated movement of contaminated seed and dispersal of inoculum, mutations and recombination as prime evolutionary processes play essential role in defining the genetic structure of BS population.

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“…It was not less, than in other studies on clonal filamentous ascomycetes with 19-21% of variability between groups 46,47 or filamentous ascomycetes with mixed reproduction mode, with 2-13% of total variability explained by differences between intraspecific groups. 48,49 Intraspecific genetic lines in fungi sometimes demonstrate restricted geographic ranges. [50][51][52][53] Here, we compiled the map of global distribution of T. rubrum genetic lineages (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Pchelin

Mochalov

Azarov

et al. 2020

Preprint

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The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T. rubrum sensu stricto and T. violaceum, as well as other less well established or debatable taxa like T. soudanense, T. kuryangei and T. megninii. We aimed to describe genetic lineages in Russian T. rubrum sensu stricto, to find whether these lineages possess specific characteristics and to identify factors, shaping the population structure. We assessed polymorphism of 12 simple sequence repeat (SSR, or microsatellite) loci and TERG_02941 protein-coding gene in 70 T. rubrum isolates and also performed phylogenomic analysis. In both cases, two genetic lineages were found. The analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22-48% of the variability was between groups within T. rubrum. The pattern of phylogenetic changes in polymorphic protein-coding loci and SSR typing results revealed the pressure of strong directional selection, but its sources remained elusive. Our results suggest that Russian population of T. rubrum consists of two cosmopolitan genetic lineages, with no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression and urease activity.HighlightsRussian population of fungal pathogen Trichophyton rubrum is formed by two global genetic lineagesPopulation structure in T. rubrum can be studied by improved microsatellite typing assay along with SNP typing and whole genome sequencingIn T. rubrum, there is seemingly no association between genetic lineages and types of infection, places of geographic origin, aldolase gene expression and urease activityIn T. rubrum, microevolution is driven by strong directional selection of yet unknown nature

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Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Ustilago hordei Causing Covered Smut of Barley

Cited by 9 publications

References 46 publications

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Molecular Diversity, Haplotype Distribution and Gene Flow of Bipolaris Sorokiniana Fungus Causing Spot Blotch Disease in Different Wheat Growing Zones

Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

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