Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes

Marco Severgnini,Stefania Chessa,Paola Cremonesi,Emanuele Capra,Matteo Ricchi,Roberta Bordoni,Bianca Castiglioni,Mario Luini,Barbara Lazzari

doi:10.1038/s41598-018-32992-0

Abstract

Prototheca zopfii (P. zopfii, class Trebouxiophyceae, order Chlorellales, family Chlorellaceae), a non-photosynthetic predominantly free-living unicellular alga, is one of the few pathogens belonging to the plant kingdom. This alga can affect many vertebrate hosts, sustaining systemic infections and diseases such as mastitis in cows. The aim of our work was to sequence and assemble the P. zopfii genotype 1 and genotype 2 mitochondrial and plastid genomes. Remarkably, the P. zopfii mitochondrial (38 Kb) and plastid (28 Kb) genomes are models of compaction and the smallest known in the Trebouxiophyceae. As expected, the P. zopfii genotype 1 and 2 plastid genomes lack all the genes involved in photosynthesis, but, surprisingly, they also lack those coding for RNA polymerases. Our results showed that plastid genes are actively transcribed in P. zopfii, which suggests that the missing RNA polymerases are substituted by nuclear-encoded paralogs. The simplified architecture and highly-reduced gene complement of the P. zopfii mitochondrial and plastid genomes are closer to those of P. stagnora and the achlorophyllous obligate parasite Helicosporidium than to those of P. wickerhamii or P. cutis. This similarity is also supported by maximum likelihood phylogenetic analyses inferences. Overall, the P. zopfii sequences reported here, which include nuclear genome drafts for both genotypes, will help provide both a deeper understanding of the evolution of Prototheca spp. and insights into the corresponding host/pathogen interactions.

Highlights

Organisms belonging to the genus Prototheca are achlorophyllous algae widespread in the environment
P. zopfii genotype 2 shows a single intron in the long ribosomal subunit gene, whereas the other species belonging to the Chlorellales (i.e.: C. variabilis, A. protothecoides, Helicosporidium sp., and P. wickerhamii) display a more complex structure, with intron length reaching 4,000–8,000 bp
Structure of the mitochondrial genomes of both P. zopfii genotypes was revealed to be smaller in size and extremely condensed when compared to that of some related organisms, i.e.: P. wickerhamii[22] and Helicosporidium sp.[43], but functional, with the size reduction mostly due to the lack of intron-exon structures

Summary

Introduction

Organisms belonging to the genus Prototheca are achlorophyllous algae widespread in the environment. The sequences of Prototheca species currently available in public databases are those of the 18S rDNA (small subunit of rDNA, SSU) and 28S rDNA (large subunit of rDNA, LSU)[2,19], and those of the Internal Transcribed Spacer regions (ITS), as well as some mitochondrial and plastid genomes This information is not available for all species and, full-length sequences are very often missing[12,20,21]: complete sequences of the organellar DNA are currently only available for P. wickerhamii (both mitochondrion and plastid)[22,23], P. cutis and P. stagnora (plastid only)[24]. For the first time, a representative overview of the extreme reduction which occurs within the mitochondrial and plastid genomes of these algae and provides basic information for further investigations

Objectives

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Conclusion