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Background  The 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.    Results  The  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.    Conclusions  This 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 material  The online version of this article (doi:10.1186/s12864-016-3480-x) contains supplementary material, which is available to authorized users.

bmc genomics

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