A Comparison of Microsatellites in Phytopathogenic Aspergillus Species in Order to Develop Markers for the Assessment of Genetic Diversity among Its Isolates

Abstract

The occurrence of Microsatellites (SSRs) has been witnessed in most of the fungal genomes however its abundance varies across species. In the present study, we analyzed the frequency of SSRs in the whole genome and transcripts of two phyto-pathogenic (Aspergillus niger and Aspergillus terreus) and compared them with two non-pathogenic (Aspergillus nidulans and Aspergillus oryzae) Aspergillus. Higher relative abundance and relative density of SSRs were observed in the whole genome and transcript sequences of the pathogenic Aspergillus when compared to the non-pathogenic. The relative abundance and density of SSRs were positively correlated with the G+C content of transcripts. Among the different classes of SSR, the percentage of tetra-nucleotide SSRs were maximum in A. niger (36.7%) and A. oryzae (35.9%) whereas A. nidulans and A. terreus preferred tri-nucleotide SSRs (38.2 and 42.1%) in whole genome sequences. In transcripts, tri-nucleotide SSRs were the most abundant whereas di-nucleotide SSRs were the least favored. Motif conservation study among the transcripts revealed conservation of only 27% motif within Aspergillus species. Furthermore, a similar relationship among the Ascomycetes was obtained on the basis of motif conservation and conserved genes (rDNA). To analyze the diversity present within the Indian isolates of Aspergillus, primers were successfully designed for 692 motifs in A. niger and A. terreus of which 20 were selected for diversity analysis. Among all the markers amplified, 10 markers (83.3%) were polymorphic, whereas remaining two markers (16.6%) were monomorphic. Ten polymorphic markers acquired in this investigation showed the utility of recently created SSR markers in the assessment of genetic diversity among various isolates of Aspergillus.

The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum

“…There was substantial evidence for non-random distribution of SSRs across protein-coding regions, UTRs, and introns ( Li et al, 2004 ; Vieira et al, 2016 ). Similar observations were made in other fungi in which trinucleotide repeats were selected as opposed to other types of SSRs in open reading frames and 5′ upstream regions, like in edible mushrooms like Pleurotus ostreatus ( Qu et al, 2016 ), forest pathogen Heterobasidion irregulare ( Gonthier et al, 2015 ), Aspergillus species ( Mahfooz et al, 2017 ) and the mycoparasitic Trichoderma species ( Mahfooz et al, 2016 ), Agaricus bisporus ( Foulongne-Oriol et al, 2013 ); and in yeast ( Richard and Dujon, 1996 ), which resembles humans in terms of distribution and stability of trinucleotide repeats ( Subramanian et al, 2003 ). Since SSRs within genes evolve through mutational processes, they have the potential to generate novel alleles at the loci harbouring them.…”

“…Construction of SSR-enriched libraries or screening of small insert genomic DNA libraries is a time, cost and labour intensive exercise. Traditional methods also have issues with reproducibility and are often not sufficient for evaluation of strain variations ( Mahfooz et al, 2017 ). With increasing number of fungal genomes being sequenced through NGS and development of a number of in silico tools, genome-wide analysis of SSRs has become much simpler and quicker.…”

“…However, there have been only limited studies on composition of SSRs in the sequenced genomes of fungi like yeast, mushrooms and some phytopathogenic fungi including Fusarium, Magnaporthe species, Aspergillus species etc. ( Lim et al, 2004 ; Wang et al, 2014 ; Qu et al, 2016 ; Mahfooz et al, 2017 ). The SSR profiles of different fungal species and strains studied so far were found to be highly specific in terms of the SSR types, frequency of occurrence, density and types of dominant motifs, independent of their genome sizes ( Karaoglu et al, 2005 ).…”

Comparative Genome-Wide Characterization of Microsatellites in <b><i>Candida albicans</i></b> and <b><i>Candida dubliniensis</i></b> Leading to the Development of Species-Specific Marker

“…It may be due to the rapid evolution and de novo production and loss of microsatellites in living organisms. Such unique microsatellite motifs were also reported in a few more fungal species [49, 50]. We utilized these unique microsatellite motifs for the development of species-specific markers.…”

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

“…However, the current study was performed on the complete genome assembly of Uh4857-4 and Uh364 isolates and non-coding sequences were also included. As a consequence, it permits to report a huge number of microsatellites (100239 in Uh364 and 137442 in Uh4857-4) compared to earlier reports in phytopathogenic fungi (Kumar et al, 2012;Singh et al, 2014a;Zhang et al, 2015;Mahfooz et al, 2017;Choudhary et al, 2018;Varady et al, 2018). In the present study, the relative abundance of microsatellites in the whole genome of Uh4857-4 (5246.27 microsatellites per Mb) and Uh364 (5125.14 microsatellites per Mb) is quite similar, suggesting the highly homogeneous genomic structure of these two U. hordei isolates.…”