Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales

Hariprasath Prakash,Arunaloke Chakrabarti,Chandan Badapanda,Shivaprakash Mandya Rudramurthy,Milner M Kumar,Anup Kumar Ghosh,Prasad S Gandham

doi:10.1186/s12864-017-4136-1

Abstract

BackgroundApophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism.ResultsThe whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins.ConclusionThe present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of pathogenic Apophysomyces species. The presence of unique CAZymes in cell wall might be exploited in future for antifungal drug development.

Highlights

Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India
The genome assembly of A. variabilis consisted of 1155 contigs and 431 scaffolds with N50 scaffold length of 647.5 kilobases (Kb) and total genome size of 39.38 Mb
The average G + C content of the three Apophysomyces genomes ranged from 41.7% to 41.9%

Summary

Introduction

Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. Mucoromycotina, a subdivision of Kingdom Fungi is currently placed in incertae sedis and comprises three orders namely Mucorales, Endogonales and Mortieriellales [1]. The current taxonomical position of fungal species under the order Mucorales is evolving with the use of molecular techniques. Spatafora et al proposed a phylum level phylogenetic classification of mucoralean fungi comprising of two phyla (Mucoromycota and Zoopagomycota), six subphyla, four classes, and 16 orders [4]. Of the known 225 species under Mucorales, approximately 20 species are known to cause human infections

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