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=13

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=<p>The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of <italic>Lentinula edodes</italic> were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated <italic>trnG1-trnG2</italic> unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from <italic>cox1, rnl</italic>, and <italic>rns</italic> of three mtDNAs. Loss of two introns in <italic>cox1</italic> of KY217797.1 reduced its size by 2.7 kb, making it the smallest <italic>cox1</italic> gene (8.4 kb) among the <italic>cox1</italic>s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in <italic>cox1</italic> of MF774813.1 resulted in the longest <italic>cox1</italic> (12 kb). In <italic>rnl</italic> of <italic>L. edodes</italic>, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the <italic>rnl</italic> size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (<italic>pol2</italic>-<italic>pol3</italic> and <italic>pol1</italic>-<italic>atp8</italic>) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at <italic>pol2</italic>-<italic>pol3</italic> region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.</p>