Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici

Abstract

Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere

“…This may be due to the ubiquitous nature and seemingly random chromosomal distribution of random repeats in Trichoderma genome, giving rise to simultaneous PCR amplification of multiple genomic regions (Rai et al 2016). The high genotypic variability among Trichoderma isolates could be associated with mutations in priming sites, rearrangements of chromosomal segments or recombination process in fungal genomes (Kumar et al 2012, 2013b). However, genetic variability among Trichoderma isolates in addition to their differences in fungal growth inhibition toward fungal plant pathogens suggest that combinations of isolates could further be applied in both greenhouse and field studies to manage tomato diseases.…”

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.…”

“…Several types of molecular markers such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSR), and singlenucleotide polymorphism (SNP) have been widely explored for understanding the genetic diversity and population structure of fungal crop pathogens (Karwasra et al, 2002;Braithwaite et al, 2004;Sun et al, 2013;Goswami et al, 2017). However, in comparison to these markers, SSR emerged as a promising marker for DNA fingerprinting, genetic linkage mapping, quantitative trait locus (QTL) identification, population genetics, and evolutionary studies owing to their polymorphic attribute, excellent reproducibility, co-dominance, and omnipresence inside the genome (Ellegren, 2004;Kumar et al, 2012;Singh et al, 2014a;Rai et al, 2016). Recently, these markers have been explored for studying various phytopathogenic fungi, such as Ustilago segetum tritici (Kashyap et al, 2019), Tilletia indica (Sharma et al, 2018), Ustilago scitaminea (Zhou et al, 2008), Ustilago maydis (Jiménez-Becerril et al, 2018), Phytophthora infestans (Montarry et al, 2010), Fusarium udum (Kashyap et al, 2015), Fusarium pseudograminearum (Scott and Chakraborty, 2010), and Colletotrichum gloeosporioides (Moges et al, 2016).…”

Novel microsatellite markers suitable for genetic studies in Polyporus umbellatus (Polyporales, Basidiomycota)

“…However, in Fusarium oxysporum f. sp. Lycopersici, tetra-nucleotide motifs had the highest accumulation (Kumar et al, 2012).…”