AUTHOR=Kim Sinil , Eom Hyerang , Nandre Rutuja , Choi Yeon Jae , Lee Hwayong , Ryu Hojin , Ro Hyeon-Su 

TITLE=Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1034387

DOI=10.3389/fmicb.2022.1034387

ISSN=1664-302X

ABSTRACT=The mitochondrial DNAs (mtDNAs) of the 21 wild and cultivated strains of Lentinula edodes were assembled and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 11.7 kbp~12.2 kbp. The gene number was observed consistent except that Cham-B17_MT has two additional tRNA gene for glycine. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. The intron number differences were found in cox1, rrnL, and rrnS from three mtDNAs. The mtDNA KY217797.1 was devoid of intron2 (1,730 bp) and intron3 (972 bp) in cox1 whereas intron2 was missing in MF774813.1. However, cox1 of the latter contained an additional 2,653 bp-long group II intron in the exon5 that made it the biggest cox1 gene among cox1s of 25 mtDNAs. rrnL had a specific sequence region, consisted of intron insertion consensus units of TTAATAGCGGTCT, TAACCATGAGGAT, and CCTAAGGTAGCA-115NTs-GGGACGGGAAG in sequential arrangement for multiple intron incorporation, which appeared to be conserved in basidiomycetes. SL10_MT lacked the second intron among the three rrnL introns, leaving the second and third intron insertion units connected. Homing endonuclease (HEG) was implied to involve in the intron mobilization since all the introns in these genes contained intron-encoding HEG genes having LAGRIDADG or GIY-YIG domains and the intron insertion sites had conserved HEG cleavage sites. Repeated sequences and TEs contributed 4.6% and 11.4% of the mtDNA, respectively. Both were mostly found in the intronic and intergenic regions. In general, the total TE content in mtDNA was higher in the cultivated strains while the strains close to wild ones showed less TE content. Different from TEs, the number of the repeated sequence units was variable in a strain-dependent manner. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kbp-long deletion at pol2-pol3 region made MF774813.1 the smallest mtDNA of all. The results showed the diversification of mtDNA in the strain level through insertion/deletion and repeating of DNA fragments, and implies mtDNA is a dynamic molecule that persistently evolves in a short time period.