A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

Abstract

Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.

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

“…Microsatellite loci show extensive length polymorphism, and hence they are widely used for DNA fingerprinting and diversity studies in bacteria (Mrazek et al, 2007 ; Guo and Mrazek, 2008 ), fungi (Kim et al, 2008 ; Araujo et al, 2012 ; Mahfooz et al, 2012a , b ), plants (Datta et al, 2010 ; Yu et al, 2017 ), and human (Subramanian et al, 2003 ; Shin et al, 2017 ). The utility of microsatellites as a molecular marker is well-known, however, its presence and absence in a particular species are of great functional and evolutionary significance (Gibbons and Rokas, 2009 ; Mahfooz et al, 2015 , 2016 ).…”

Genomewide identification and development of microsatellite markers for Marssonina brunnea and their applications in two populations

“…Microsatellites have become an important and extensively used tool in genetic studies (Sollars et al., ; Vieira et al., ). Recently, microsatellite markers have been developed for various fungal species and used for elucidating different genetic phenomena (Busse et al., ; Mahfooz et al., ; Yu et al., ). The analysis of microsatellite distribution is fundamental to their application in other research studies (Mahfooz et al., ; Yu et al., ).…”

“…Recently, microsatellite markers have been developed for various fungal species and used for elucidating different genetic phenomena (Busse et al., ; Mahfooz et al., ; Yu et al., ). The analysis of microsatellite distribution is fundamental to their application in other research studies (Mahfooz et al., ; Yu et al., ). Among the nine fungal pathogens examined in this study, the genome of M. brunnea showed the highest number of SSR loci.…”

“…Elucidating the genetic diversity and population structure of pathogens can facilitate a better understanding of the potential occurrence of outbreaks and development of host resistance (Mcdonald & Linde, 2002 Microsatellites have become an important and extensively used tool in genetic studies (Sollars et al, 2017;Vieira et al, 2016). Recently, microsatellite markers have been developed for various fungal species and used for elucidating different genetic phenomena (Busse et al, 2017;Mahfooz et al, 2016;Yu et al, 2016). The analysis of microsatellite distribution is fundamental to their application in other research studies (Mahfooz et al, 2016;Yu et al, 2016).…”

“…To evaluate the feasibility of microsatellite marker development in M. brunnea, we analysed the distribution of SSRs in M. brunnea relative to that of other eight important fungal pathogens that also have complete genome sequences. Additionally, many studies also analysed microsatellite distribution before developing SSRs markers (Mahfooz et al, 2016;Yu et al, 2016;Zhao et al, 2015). Assessing the distribution of microsatellites in M. brunnea might provide valuable information for further marker development.…”