Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum

Abstract

BackgroundThe fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequence of P. lilacinum. The study aims to decipher the putative genetic components of the fungus involved in nematode pathogenesis by performing comparative genomic analysis with nine closely related fungal species in Hypocreales.Resultsde novo genomic assembly was done and a total of 301 scaffolds were constructed for P. lilacinum genomic DNA. By employing structural genome prediction models, 13, 266 genes coding for proteins were predicted in the genome. Approximately 73 % of the predicted genes were functionally annotated using Blastp, InterProScan and Gene Ontology. A 14.7 % fraction of the predicted genes shared significant homology with genes in the Pathogen Host Interactions (PHI) database. The phylogenomic analysis carried out using maximum likelihood RAxML algorithm provided insight into the evolutionary relationship of P. lilacinum. In congruence with other closely related species in the Hypocreales namely, Metarhizium spp., Pochonia chlamydosporia, Cordyceps militaris, Trichoderma reesei and Fusarium spp., P. lilacinum has large gene sets coding for G-protein coupled receptors (GPCRs), proteases, glycoside hydrolases and carbohydrate esterases that are required for degradation of nematode-egg shell components. Screening of the genome by Antibiotics & Secondary Metabolite Analysis Shell (AntiSMASH) pipeline indicated that the genome potentially codes for a variety of secondary metabolites, possibly required for adaptation to heterogeneous lifestyles reported for P. lilacinum. Significant up-regulation of subtilisin-like serine protease genes in presence of nematode eggs in quantitative real-time analyses suggested potential role of serine proteases in nematode pathogenesis.ConclusionsThe data offer a better understanding of Purpureocillium lilacinum genome and will enhance our understanding on the molecular mechanism involved in nematophagy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2229-2) contains supplementary material, which is available to authorized users.

Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes

“…In addition, a previous study from rocks in the Atacama Desert reported the presence of some pathogenic Aspergillus species [19]. We also detected contigs related to Purpureocillium lilacinum, a species of filamentous fungus from the family Ophiocordycipitaceae (class Sordariomycetes) that has been isolated from deserts and which has demonstrated good potential as a biocontrol agent [26].…”

<i>Esteya Vermicola</i>, a Nematophagous Fungus Attacking the Pine Wood Nematode, Harbors a Bacterial Endosymbiont Affiliated with <i>Gammaproteobacteria</i>

“…Endobacteria present between two layers of the envelope may produce and secrete enzymes essential for adhesion to or the penetration of the nematode’s body wall, which comprises substances between the two layers of the envelope of a mature lunate spore. The harbored endobacteria make E. vermicola very different from other nematophagous fungi ( 22 , 24 , 26 , 30 , 41 , 57 ), and this may result in a distinctive nematophagous mechanism for E. vermicola . Therefore, endobacteria may play prominent roles in shaping the formation of lunate spores, which influences nematocidal function, thereby contributing to further ecological success.…”

Managing the plant microbiome for biocontrol fungi: examples from Hypocreales

“…Several of these species have been developed for commercially available products including Hirsutella minnesotensis, Pochonia chlamydosporia and Purpureocillium lilacinum [49]. All three of these species are natural inhabitants of soil environments and genome sequence data exists for representative isolates [50][51][52][53].…”