Comparative mitochondrial genome analyses reveal conserved gene arrangement but massive expansion/contraction in two closely related Exserohilum pathogens

The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny

In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.

First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Endophytic fungi play an important role in the growth and development of traditional Chinese medicine plants. We isolated a strain of Acrocalymma vagum from the endophytic fungi of the traditional Chinese plants Paris. To accurately identify this endophytic fungal species of interest, we sequenced the mitochondrial genome of A. vagum, which is the first discovered mitochondrial genome in Massarineae. The A. vagum mitochondrial genome consists of a 35,079-bp closed circular DNA molecule containing 36 genes. Then, we compared the general sequence characteristics of A. vagum with those of Pleosporales, and the second structure of the 22 tRNAs was predicted. The phylogenetic relationship of A. vagum was constructed using two different data sets (protein-coding genes and amino acids). The phylogenetic tree shows that A. vagum is located at the root of Pleosporales. The analysis of introns shows that the number of introns increases with the increase in branch length. The results showed that monophyly was confirmed for all families in Pleosporales except for Pleosporaceae. A. vagum is an ancient species in the Pleosporales, and Pleosporaceae may require further revision. In Pleosporales, the number of introns is positively correlated with branch length, providing data for further study on the origin of introns.

Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species

In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.

The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns

Introduction

Many members of the Ophiostomatales are of economic importance as they are bark-beetle associates and causative agents for blue stain on timber and in some instances contribute towards tree mortality. The taxonomy of these fungi has been challenging due to the convergent evolution of many traits associated with insect dispersal and a limited number of morphological characters that happen to be highly pleomorphic. This study examines the mitochondrial genomes for three members of Leptographium sensu lato [Leptographium aureum (also known as Grosmannia aurea), Grosmannia fruticeta (also known as Leptographium fruticetum), and Leptographium sp. WIN(M)1376)].

Methods

Illumina sequencing combined with gene and intron annotations and phylogenetic analysis were performed.

Results

Sequence analysis showed that gene content and gene synteny are conserved but mitochondrial genome sizes were variable: G. fruticeta at 63,821 bp, Leptographium sp. WIN(M)1376 at 81,823 bp and L. aureum at 104,547 bp. The variation in size is due to the number of introns and intron-associated open reading frames. Phylogenetic analysis of currently available mitochondrial genomes for members of the Ophiostomatales supports currently accepted generic arrangements within this order and specifically supports the separation of members with Leptographium-like conidiophores into two genera, with L. aureum grouping with Leptographium and G. fruticeta aligning with Grosmannia.

Discussion

Mitochondrial genomes are promising sequences for resolving evolutionary relationships within the Ophiostomatales.

Genetic diversity and structure of Bipolaris oryzae and Exserohilum rostratum populations causing brown spot of rice in Burkina Faso based on genotyping-by-sequencing

In recent years, Brown spot disease of rice (BSR) has been observed on leaves and seeds of rice in all rice-growing areas of Burkina Faso. Bipolaris oryzae and Exserohilum rostratum are the main fungal species isolated from BSR infected tissues and they are frequently observed in the same field. However, we are lacking information on the genetic diversity and population structure of these fungi in Burkina Faso. The mode of reproduction is also unknown. The genetic diversity of isolates of B. oryzae (n=61) and E. rostratum (n=151), collected from major rice-growing areas of Burkina Faso, was estimated using genotyping-by-sequencing (GBS). The mean values for nucleotide diversity (π) were 1.9 x10^-4 for B. oryzae and 4.8 x10^-4 for E. rostratum. There is no genetic differentiation between the geographical populations of each species. The analysis of molecular variance revealed that 89% and 94% of the genetic variances were within the populations of B. oryzae and E. rostratum, respectively. For each species, four genetic clusters were identified by two clustering methods (DAPC and sNMF). The distribution of these genetic groups was independent of the geographical origin of the isolates. Evidence of recombination was detected in the populations of B. oryzae and E. rostratum. For B. oryzae balanced mating type ratios were supporting sexual reproduction. For E. rostratum overrepresentation of MAT1-2 isolates (79%) suggested a predominant asexual reproduction. This study provides important information on the biology and genetics of the two major fungi causing brown spot disease of rice in Burkina Faso.