Comparative analysis of the mitochondrial genome of the fungus Colletotrichum lindemuthianum, the causal agent of anthracnose in common beans

Abstract

Fungi of the genus Colletotrichum are economically important and are used as models in plant-pathogen interaction studies. In this study, the complete mitochondrial genomes of two Colletotrichum lindemuthianum isolates were sequenced and compared with the mitochondrial genomes of seven species of Colletotrichum. The mitochondrial genome of C. lindemuthianum is a typical circular molecule 37,446 bp (isolate 89 A 2-3) and 37,440 bp (isolate 83.501) in length. The difference of six nucleotides between the two genomes is the result of a deletion in the ribosomal protein S3 (rps3) gene in the 83.501 isolate. In addition, substitution of adenine for guanine within the rps3 gene in the mitochondrial genome of the 83.501 isolate was observed. Compared to the previously sequenced C. lindemuthianum mitochondrial genome, an exon no annotated in the cytochrome c oxidase I (cox1) gene and a non-conserved open reading frame (ncORF) were observed. The size of the mitochondrial genomes of the seven species of Colletotrichum was highly variable, being attributed mainly to the ncORF, ranging from one to 10 and also from introns ranging from one to 11 and which encode a total of up to nine homing endonucleases. This paper reports for the first time by means of transcriptome that then ncORFs are transcribed in Colletotrichum spp. Phylogeny data revealed that core mitochondrial genes could be used as an alternative in phylogenetic relationship studies in Colletotrichum spp. This work contributes to the genetic and biological knowledge of Colletotrichum spp., which is of great economic and scientific importance.

Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita

“…These features make it suitable for distinguishing closely related species or even intra-specific isolates, as well as deduction of recent evolutionary events. Intra-specific mtDNA comparison has been used in fungal species such as Cordyceps militaris [24] , Schizosaccharomyces pombe [25] , Isaria cicadae [10] , and Colletotrichum lindemuthianum [26] . These studies provided new insights into population evolution, identification of highly polymorphic regions, and isolate-specific markers [24] .…”

Revisiting the Neurospora crassa mitochondrial genome

“…2017; de Queiroz et al . 2018), but was not observed in N. crassa . Nevertheless, the start codon of nd2 is immediately after the stop codon of nd3 with no intergenic sequence between both genes.…”

“…2008) and Colletotrichum lindemuthianum (de Queiroz et al . 2018). The longest overlap (658 bp) occurs between NADH dehydrogenase subunit 4 and a laglidadg endonuclease.…”

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

“…of Colletotrichum species are due, in part, to the presence or absence of ncORFs and intronic sequences [66]. The large mtDNA size of Phlebia radiata (156 kbp) also harbors a large number of introns and long intergenic regions [63].…”

“…Many of the ncORFs were related to HEGS, primarily LAGLIDADG endonucleases. Queiroz et al [66] observed that C. lindemuthianum contains just one intronic ncORF encoding a LAGLIDADG endonuclease. However, more than one intronic ncORF encoding LAGLIDADG endonucleases were found in rust mtDNA.…”