Structural characterization and evolutionary analyses of theCoccidioides immitisandCoccidioides posadasiimitochondrial genomes

Abstract

Fungal mitochondrial genomes encode for genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and these genes have been used as molecular markers for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, almost one hundred Coccidioides strains have been sequenced. The focus of these studies has been exclusively to infer patterns of variation of nuclear genomes (nucDNA). However, their mitochondrial genomes (mtDNA) have not been studied. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 published genomes. The circular-mapping mtDNA molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identified the fourteen mitochondrial protein-coding genes common to most fungal mitochondria, including genes encoding the small and large ribosomal RNAs (rns and rnl), the RNA subunit of RNAse P (rnpB), and 26 tRNAs organized in polycistronic transcription units, which are mostly syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparison of the mtDNA and nucDNA genomes shows discordance, possibly due to differences in patterns of inheritance. In summary, this work represents the first complete assessment of mitochondrial genomes among several isolates of both species of Coccidioides, and provides a foundation for future functional work.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction

“…As a result, mapping RNAseq reads or splice-aligning assembled transcripts to the genome sequence often generates conflicting information that interferes with or misleads gene modelling. In the example shown in Figure 1 [data from (de Melo Teixeira et al, 2021)], expert inference of the gene structure was only possible by sequence comparison with intron-less gene homologs in related species.…”

“…The output of MFannot lists gene coordinates either in a format that can be directly loaded into NCBI sequence submission tools or in 'masterfile' format (a computer-parsable and Mapping of RNA-seq data to the mitochondrial genome of Coccidioides posadasii. The figure depicts a 2,579 nt window over the coordinates of exons 4 (6172-6736) and 5 (8458-8504) of the mitochondrial gene encoding the large subunit rRNA (rnl) of C. posadasii (see (de Melo Teixeira et al, 2021) for details on genome sequencing) as determined by rRNA sequence conservation and structural modelling of exons 4 and 5 plus adjacent introns. The read-mapping coverage distribution (grey) is shown below the annotated exons.…”