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.
Highlights
The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes
Global genome structure The P. lilacinum genome was sequenced to 200 x coverage and by mapping the reads to contigs, the genome sequence was assembled into 301 scaffolds with total gap size of 526,913 bases
Core Eukaryotic Genes Mapping (CEGMA) [26, 27] analysis against a set of 248 conserved protein families that occur in a wide range of core eukaryotic gene datasets (CEGs) http://korflab.ucdavis.edu/Datasets /genome completeness/index.html#SCT2) found 96.77 % of the core genes were matched, indicating that the draft genome sequence of P. lilacinum was largely complete (Additional file 1: Table S1). tRNAScan-SE [28, 29] predicted a total of 91 tRNAs in the genome
Summary
The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. Purpureocillium lilacinum, previously named as Paecilomyces lilacinus, belongs to the fungal order Hypocreales that harbors species known to produce a diversity of secondary metabolites and bio-actives [1]. The fungal order Hypocreales consists of plantpathogens, insect-pathogens, nematode-pathogens, plantendophytes and mycoparasites. These fungi are multitrophic in nature and several transitions between lifestyles have been predicted in their evolutionary history [13,14,15]. P. lilacinum is reported to exercise parasitic or endophytic lifestyles in the presence of a host organism such as nematodes, aphids and cotton plants (Gossypium hirsutum) [9,10,11,12]
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