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Background   Sarocladium brachiariae  is a newly identified endophytic fungus isolated from  Brachiaria brizantha . A previous study indicated that  S. brachiariae  had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of  S. brachiariae  and compared it with the genome of  S. oryzae  to identify differences between a  Sarocladium  plant pathogen and an endophyte.    Results  In this study, we reported a gapless genome sequence of a newly identified endophytic fungus  Sarocladium brachiariae  isolated from  Brachiaria brizantha . The genome of  S. brachiariae  is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of  S. brachiariae  and its closest species was identified as  S. oryzae . Comparative genomics analysis revealed that  S. brachiaria  has 14.9% more plant cell wall degradation related CAZymes to  S. oryzae , and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of  S. brachiaria . Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in  S. oryzae . However,  S. brachiaria  had seven fewer terpene gene clusters, including helvolic acid BGC, compared with  S. oryzae  and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between  S. brachiariae  and  S. oryzae  revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the  S. brachiariae  could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity.    Conclusions  The data provided a better understanding of the  Sarocladium brachiariae  genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae