Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus

Abstract

Simple sequence repeats (SSRs) play specific roles in many biological activities. In this paper, we focused on SSRs in the genome of Pleurotus ostreatus, which is a widely cultivated edible mushroom. The distribution curves of SSRs and exons are opposite throughout the genome, which means that SSRs are mostly located in non-coding regions. A comparative analysis of nine fungi suggests that Agaricomycotina fungi have similar SSR distributions. Functional enrichment analysis on the SSR-containing gene set uncovers enriched functions about environmental interactions and important cellular functions for life. Trinucleotide SSRs account for an extremely high fraction of all SSRs, and in exonic regions, they are equivalent to inserting repeating amino acids (RAAs) into the protein sequences. The RAA indel could partly explain some enriched functions of the genes they modify. Agaricomycotina fungi have similar distributions of RAAs, indicating that this may be a potential common mechanism for some specific functions.

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.…”

“…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 ).…”

Utilization of Some Agro-Wastes for Cultivation of <i>Pluerotus ostreatus</i> (Oyster Mushroom) in Keffi Nigeria

“…The Pleurotus ostreatus can be widely cultivated, and it can adapt to different temperatures. It exists on every continent except Antarctica and grows throughout the year [46].…”

Characterization of simple sequence repeats in the Pleurotus ostreatus cultivars, 'Heuktari' and 'Miso'

“…SSR의 생물학적 기능에 대한 연구에 따 르면, 이들은 세균의 기주내 환경적응에 활용되고 (Moxon et al, 2006), 인간 질병의 원인, 진화과정이나 유전자 발 현조절에 관여하는 것으로 보고되었다 (Benson, 1999). 균 류에서의 SSR의 역할에 대한 연구는 몇몇 균주에 대해 한정적으로 연구되었는데 (Karaoglu et al, 2004;Labbé et al, 2011), 느타리버섯 유전체내의 초위성체는 대부분 exon외에 존재하여 유전자 사이의 영역에 존재하는 것으 로 예측되었다 (Qu et al, 2016). 유전체가 복제될 때 다양 한 요인으로 인하여 복제효소의 작용으로 SSR에 돌연변 이가 생길 수 있는데 (Chistiakov et al, 2005), 이때 반복 서열이 더해지거나 빠져나감으로써 SSR의 크기가 달라질 수 있다 (Wei et al, 2015).…”