Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato: insights into the evolution of a fungal species complex interacting with diverse plants. (December 2017)

• Record Type: Journal Article
• Authors: Liang, Xiaofei; Tian, Xianglin; Liu, Wenkui; Wei, Tingyu; Wang, Wei; Dong, Qiuyue; Wang, Bo; Meng, Yanan; Zhang, Rong; Gleason, Mark; Sun, Guangyu
• Is Part Of: BMC genomics. Volume 18:Number 1(2017)
• Page Start: 1
• Page End: 16
• Publication Date: 2017-12
• Subjects: Evolution -- Species complex -- Mitochondrial genome -- Concatenation -- Phylogeny; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3480-x
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background The fungal species complexColletotrichum 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 inC. 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 fourC. gloeosporioides s.l. species lineages (C.gloeosporioides, C. fructicola, C. aenigma, andC. siamense s.l.), and evaluated the usefulness of mitogenome sequence in complementing prevailing nuclear markers for species delimitation. Results TheC. 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 reportedColletotrichum 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 nascentC. siamense s.l. complex. The tree topology was highly congruent with the phylogeny based on nuclear marker concatenation except for lineages withinC. 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 ofC. 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 withC. gloeosporioides s.l. and otherColletotrichum species.