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Title: Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests short fragment insertions as a potential factor leading to larger genomic size

Author
item DENG, YOUJIN - Fujian Agricultural & Forestry University
item HSIANG, TOM - University Of Guelph
item Li, Shuxian
item LIN, LONGJI - Fujian Agricultural & Forestry University
item WANG, QING-FU - Fujian Agricultural & Forestry University
item CHEN, QINGHE - Fujian Agricultural & Forestry University
item XIE, BAOGUI - Fujian Agricultural & Forestry University
item MING, RAY - University Of Illinois

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/14/2018
Publication Date: 9/10/2018
Publication URL: https://handle.nal.usda.gov/10113/6472449
Citation: Deng, Y., Hsiang, T., Li, S., Lin, L., Wang, Q., Chen, Q., Xie, B., Ming, R. 2018. Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests short fragment insertions as a potential factor leading to larger genomic size. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.02079.
DOI: https://doi.org/10.3389/fmicb.2018.02079

Interpretive Summary: Silver-ear mushroom is very popular in the cuisine and medicine of East Asia. Success in the cultivation of this mushroom requires two different fungi (Tremella fuciformis and Annulohypoxylon stygium) growing together. However, like siblings, not all isolates of those two fungi are compatible. Without successfully compatible pairing of two fungi, the mushroom can not be formed. As a first step to investigate the mechanism of the compatibility of two fungi and formation of the mushroom, comparisons of the genetic differences among isolates were conducted using modern scientific methods. It was found that small genetic modifications could cause different genome sizes of isolates in the second fungus. Further study will be conducted to determine if the larger genomes are reliably associated with the isolates of this fungus that do better in the companion roles.

Technical Abstract: Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium were assembled from raw reads from PacBio and Illumina sequencing. Comparisons of mtDNAs of six isolates were conducted to analyze the diversity of genomic structures, conserved genes, intergenic regions and introns. Mitochondrial genomes of six isolates of A. stygium ranged from 132 kb to 147 kb in size, contained same sets of conserved protein-coding, tRNA and rRNA genes, and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar size except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes. Sixty-six intron insertion sites and 100 different introns were detected in these genomes. Each genome contained more than 46 introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns within the same insertion site revealed some complex introns, such as twintrons and orf-less introns. There were 45 short fragment insertions which were detected within introns, intergenic regions, or as introns, some of them located at critical conserved domain regions in the intron. Insertions of short fragment such as small inverted repeats might affect or hinder the movement of introns, which allow for intron accumulation in mitochondrial genomes, and enlarge their size. This study revealed that the evolution of fungal mitochondrial introns was complex, and the results suggested short fragment insertions as potential sources of large mitochondrial genomes in A. stygium.