Abstract

BackgroundColourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529.ResultsThe assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome.ConclusionsOverall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.

Highlights

  • Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans

  • General features of the P. wickerhamii nuclear genome Nuclear genome assembly and quality assessment Sequencing of the P. wickerhamii chromosome produced a total of 2,429,822,821 and 2,198,163,916 nucleotides and 8,239,274 and 286,004 reads for Illumina and PacBio, respectively

  • The high quality of the genome assembly was confirmed with the BUSCO analysis (Supplementary Figure S1)

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Summary

Introduction

Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. The chlorophytan genus Prototheca contains aerobic, unicellular, colourless, yeast-like algae, able to cause disease in humans and other mammals, referred to as protothecosis. Among all the Viridiplantae, only Prototheca and Chlorella microalgae possess a pathogenic potential for both humans and animals [1,2,3,4]. The Prototheca spp. are accepted to belong to the family Chlorellaceae of the order Chlorellales, in the class Trebouxiophyceae. Their closest photosynthetic relative is Auxenochlorella protothecoides [7]. The Helicosporidia seem to be basal to the A. protothecoides and Prototheca clades, implying that the loss of photosynthesis must have occurred at least twice in the evolution of heterotrophic Chlorellales [7]

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