Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato: insights into the evolution of a fungal species complex interacting with diverse plants

Abstract

BackgroundThe fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex’s host-interaction biology. In this study, we first sequenced and compared nine mitogenomes belonging to four C. gloeosporioides s.l. species lineages (C. gloeosporioides, C. fructicola, C. aenigma, and C. siamense s.l.), and evaluated the usefulness of mitogenome sequence in complementing prevailing nuclear markers for species delimitation.ResultsThe C. gloeosporioides s.l. mitogenomes ranged between 52,671 and 58,666 bp in size, and each contained an identical set of genes transcribed in the same direction. Compared with previously reported Colletotrichum mitogenomes, these mitogenomes were uniquely featured by: (1) significantly larger genome size due to richer intron content and longer intergenic region; (2) striking GC content elevation at the intergenic region; and (3) considerable intron content variation among different species lineages. Compared with nuclear DNA markers commonly used in phylogeny, the mitogenome nucleotide diversity was extremely low, yet the mitogenome alignment contained the highest number of parsimony informative sites, which allowed the generation of a high-resolution phylogeny recognizing all taxonomic lineages, including ones belonging to the very nascent C. siamense s.l. complex. The tree topology was highly congruent with the phylogeny based on nuclear marker concatenation except for lineages within C. siamense s.l. Further comparative phylogenetic analysis indicated that lineage-specific rapid divergence of GS and SOD2 markers confounded concatenation-based species relationship inference.ConclusionsThis study sheds light on the evolution of C. gloeosporioides s.l. mitogenomes and demonstrates that mitogenome sequence can complement prevailing nuclear markers in improving species delimitation accuracy. The mitogenome sequences reported will be valuable resources for further genetic studies with C. gloeosporioides s.l. and other Colletotrichum species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3480-x) contains supplementary material, which is available to authorized users.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus

“…Therefore, mitogenomic sequences might be useful tools for accurate species identification 57 . In comparison to species identifications based on phylogenetic analyses of single gene sequences, such as ITS or rRNA genes 14 , 15 , phylogenies based on combined mitochondrial genes are more reliable, because they include more genetic information 58 , 59 . Here, we inferred the phylogenetic relationships of 18 species of fungi based on 15 mitogenomic PCGs; this analysis recovered a well-supported tree topology divided into three main clusters, consistent with traditional morphological classifications.…”

Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes

“…Today, the growing body of mitogenome data suggests that variation in MGE number can follow the divergence of different fungal taxa (Brankovics et al, 2017;Liang et al, 2017;Fourie et al, 2018), offering great perspectives for future diagnostic purposes. Brankovics et al (2017) showed that mosaicism in intron patterns can support the separation of three phylogenetic species in F. oxysporum.…”

“…Fourie et al (2018) revealed significant differences in intron patterns among species from the Fusarium fujikuroi species complex (FFSC). Beyond Fusarium, recent studies on Colletotrichum mitogenomes indicated that intron content variation could improve cryptic species delimitation within this genus (Liang et al, 2017).…”

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