AUTHOR=Lin Runmao , Xia Yuan , Liu Yao , Zhang Danhua , Xiang Xing , Niu Xianyu , Jiang Linjia , Wang Xiaolin , Zheng Aiping 

TITLE=Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.707281

DOI=10.3389/fmicb.2021.707281

ISSN=1664-302X

ABSTRACT=<p>Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. <italic>Rhizoctonia solani</italic>, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published <italic>Rhizoctonia</italic> mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five <italic>Rhizoctonia</italic> sp. mitogenomes). These mitogenomes encoded 15 typical proteins (<italic>cox1-3</italic>, <italic>cob</italic>, <italic>atp6</italic>, <italic>atp8-9</italic>, <italic>nad1-6</italic>, <italic>nad4L</italic>, and <italic>rps3</italic>) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (<italic>Rhizoctonia</italic> sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the <italic>rps3</italic> gene in 10 <italic>Rhizoctonia</italic> mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven <italic>R. solani</italic> and other five <italic>Rhizoctonia</italic> sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of <italic>R. solani</italic> had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the <italic>R. solani</italic> clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of <italic>rps3-nad2</italic> and <italic>nad1-m3g18</italic>/<italic>mag28</italic> (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of <italic>R. solani</italic> mitogenomes.</p>