Genomic Analysis Of The Nematophagous Fungus Pochonia Chlamydosporia

Pochonia chlamydosporia is one of the most promising biological control agents of plant nematodes which cause serious economic losses in agriculture worldwide. Studies on evolutionary relationships between Pochonia chlamydosporia and other fungi in Pezizomycotina, association between Pochonia chlamydosporia and its living environment and host, as well as pathogenic factors and pathogenic mechanisms of Pochonia chlamydosporia, are very important and valuable. In the development of biological sciences, genetics, biochemistry, comparative genomics and bioinformatics provide useful tools for research. And based on these tools, genomic research of Pochonia chlamydosporia may improve the development of research on Pochonia chlamydosporia and other related subjects.Here, we obtain the first complete mitogenome of Pochonia chlamydosporia with the length of 25,615 bp after sequencing and assembling. The mitogenome contains 40 genes, including 15 ORFs (cox1-3, cob, atp6, atp8-9, nadl-6, nad4L, rps3),2 rRNA genes (rnl and rns) and 23 tRNA genes. A maximum likelihood phylogenetic tree is constructed based on 14 ORFs, which indicates that Pochonia chlamydosporia is more closely related to Metarhizium anisopliae than other fungi with bootstrap value of 100. The evolutionary relationships show that Pochonia chlamydosporia, the entomopathogenic fungi and plant pathogens share a most recent common ancestor. The syntenic analyses show that 87.20% of Pochonia chlamydosporia mitochondrial (mt) sequences match to 90.05% of Metarhizium anisopliae mt sequences in 10 blocks, while mt sequences of other fungi match to less than or equal to 61.07% mt sequences of Pochonia chlamydosporia. A comparison of mt genomes of Pochonia chlamydosporia and other fungi in clavicipitaceae presents that their protein-coding genes are in the same order, but their genomes are variant in size. We find that protein-coding regions, intergenic regions and introns are three primary factors contributing to size variation. Additionally, rps genes that play important roles in ribosome biogenesis and DNA repair present unique evolutionary characteristics, and singals of positive selection are detected in rps genes.We also obtain a high quality draft sequence of nuclear genome of Pochonia chlamydosporia with the size of 43.9 Mb and a scaffold N50 value of 4.1 Mb. About 5.24% of genome sequences are repetitive sequences, and 15009 ORFs (70.7% are annotated genes) are predicted. A comparison of the nematophagous fungus, the entomopathogenic fungi and the plant pathogen shows that Pochonia chlamydosporia and Metarhizium anisopliae, Beauveria bassiana share more gene families, and for KOG cluster annotation, gene counts in Pochonia chlamydosporia range between counts in the plant pathogen and counts in the entomopathogenic fungi. The analysis shows that there are plenty of pathogenic factors in Pochonia chlamydosporia, including 66 P450 enzymes (51 families),68 ABC transporters (33 pathogen host interaction, PHI genes),1551 secreted proteins (hydrolytic enzymes, G protein coupled receptors, toxins, hydrophobin, chitin binding proteins, and other functional proteins are included; and among these genes,120 small cysteine-rich secreted proteins are identified),247 proteases (serine proteases that have similar function as VCP1, saccharolysin, neurolysin, and other proteases). The comparison of glycoside hydrolases and carbohydrate esterases displays three major classes of enzymes:one class is enriched with proteins in the nematophagous fungus, the second class is enriched with proteins in the nematophagous fungus and the entomopathogenic fungus, and the third class is enriched with proteins in plant pathogen and Pochonia chlamydosporia that is known as the nematophagous fungi and the endophytic fungi, which indicates that the distribution of functional genes are associated with fungal biological characteristics and functions. Additionally,56 secondary metabolism genes are found. Among these secondary metabolism clusters, a novel gene containing ankyrin repeat domain which regulates protein-protein interaction is identified in the radicicol gene cluster, and this ankyrin repeat protein may involve in radicicol biosynthesis. Moreover, at least 10 clusters containing P450 enzymes or transporters are found.In summary, the analysis of the mitogenome is expected to open new avenues for understanding the evolution of invertebrate-pathogenic fungi and comparing genomics of Pochonia chlamydosporia. The further analyses of relationships between virulence and mitogenomes may become possible based on the methods using in mammal mitogenomes analyses. Meanwhile, the analysis of the nuclear genome and the comparative analyses may established a foundation for further exploration of its biological sciences including pathogenic factors and mechanisms, interactions between pathogen, hosts and environments. And the results can provide eludes for further research on biological control.