Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans

Abstract

Ilyonectria destructans is a pathogenic fungus causing root rot and other symptoms on trees and many crops. This paper analyses the mitochondrial genome of I. destructans and compares it with other published Nectriaceae mitogenomes. The I. destructans mitogenome appears as a circular DNA molecule of 42,895 bp and an overall GC content of 28.23%. It contains 28 protein-coding genes (15 core protein genes and 13 free-standing ORFs), two rRNAs and 27 tRNAs. The gene content and order were found to be conserved in the mitogenome of I. destructans and other Nectriaceae, although the genome size varies because of the variation in the number and length of intergenic regions and introns. For most core protein-coding genes in Nectriaceae species, Ka/Ks < 1 indicates purifying selection. Among some Nectriaceae representatives, only the rps3 gene was found under positive selection. Phylogenetic analyses based on nucleotide sequences of 15 protein-coding genes divided 45 Hypocreales species into six major clades matching the families Bionectriaceae, Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae. I. destructans appeared as a sister species to unidentified Ilyonectia sp., closely related to C. ilicicola, N. cinnabarina and a clad of ten Fusarium species and G. moniliformis. The complete mitogenome of I. destructans reported in the current paper will facilitate the study of epidemiology, biology, genetic diversity of the species and the evolution of family Nectriace and the Hypocreales order.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

“…8 . Consistent with most of the currently studied mitogenomes 10 , 53 , 54 , the use of both two- and four-fold degenerate codons was biased toward the use of codons abundant in A or T. In P. serratifolia , 14,333 amino acids were encoded. The most frequently used amino acids were Leu (7.1%), Arg (6.3%), and Ser (6.1%), and the least common amino acids were Trp (1.4%) and Met (1%) (Fig.…”

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

“…In this study, we calculate the Ka/Ks values of 30 PCGs shared by the C. pubescens mitogenome and the mitogenomes of three peppers (KJ865409, KJ865410, and MN196478) using TBtools software (Table S12). Following a previous study, we change the part of the gene with Ka/Ks ratio that does not apply (NA) to zero (Androsiuk et al 2022). The results indicate that the PCGs shared by C. pubescens and the other three peppers are close homologs because most PCGs have zero Ka and Ks values.…”