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Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution

Jian Guo, Jianbo Jian, Lili Wang, Lijuan Xiong, Huiping Lin, Ziyi Zhou, Eva C. Sonnenschein Orcid Logo, Wenjuan Wu

Frontiers in Cellular and Infection Microbiology, Volume: 12

Swansea University Author: Eva C. Sonnenschein Orcid Logo

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DOI (Published version): 10.3389/fcimb.2022.797017

Abstract

The Prototheca alga is the only chlorophyte known to be involved in a series of clinically relevant opportunistic infections in humans and animals, namely, protothecosis. Most pathogenic cases in humans are caused by Prototheca wickerhamii. In order to investigate the evolution of Prototheca and the...

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Published in: Frontiers in Cellular and Infection Microbiology
ISSN: 2235-2988
Published: Frontiers Media SA 2022
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URI: https://cronfa.swan.ac.uk/Record/cronfa61715
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In order to investigate the evolution of Prototheca and the genetic basis for its pathogenicity, the genomes of two P. wickerhamii strains S1 and S931 were sequenced using Nanopore long-read and Illumina short-read technologies. The mitochondrial, plastid, and nuclear genomes were assembled and annotated including a transcriptomic data set. The assembled nuclear genome size was 17.57 Mb with 19 contigs and 17.45 Mb with 26 contigs for strains S1 and S931, respectively. The number of predicted protein-coding genes was approximately 5,700, and more than 96% of the genes could be annotated with a gene function. A total of 2,798 gene families were shared between the five currently available Prototheca genomes. According to the phylogenetic analysis, the genus of Prototheca was classified in the same clade with A. protothecoides and diverged from Chlorella ~500 million years ago (Mya). A total of 134 expanded genes were enriched in several pathways, mostly in metabolic pathways, followed by biosynthesis of secondary metabolites and RNA transport. Comparative analysis demonstrated more than 96% consistency between the two herein sequenced strains. At present, due to the lack of sufficient understanding of the Prototheca biology and pathogenicity, the diagnosis rate of protothecosis is much lower than the actual infection rate. 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spelling 2022-11-04T17:53:44.8810832 v2 61715 2022-10-31 Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2022-10-31 SBI The Prototheca alga is the only chlorophyte known to be involved in a series of clinically relevant opportunistic infections in humans and animals, namely, protothecosis. Most pathogenic cases in humans are caused by Prototheca wickerhamii. In order to investigate the evolution of Prototheca and the genetic basis for its pathogenicity, the genomes of two P. wickerhamii strains S1 and S931 were sequenced using Nanopore long-read and Illumina short-read technologies. The mitochondrial, plastid, and nuclear genomes were assembled and annotated including a transcriptomic data set. The assembled nuclear genome size was 17.57 Mb with 19 contigs and 17.45 Mb with 26 contigs for strains S1 and S931, respectively. The number of predicted protein-coding genes was approximately 5,700, and more than 96% of the genes could be annotated with a gene function. A total of 2,798 gene families were shared between the five currently available Prototheca genomes. According to the phylogenetic analysis, the genus of Prototheca was classified in the same clade with A. protothecoides and diverged from Chlorella ~500 million years ago (Mya). A total of 134 expanded genes were enriched in several pathways, mostly in metabolic pathways, followed by biosynthesis of secondary metabolites and RNA transport. Comparative analysis demonstrated more than 96% consistency between the two herein sequenced strains. At present, due to the lack of sufficient understanding of the Prototheca biology and pathogenicity, the diagnosis rate of protothecosis is much lower than the actual infection rate. This study provides an in-depth insight into the genome sequences of two strains of P. wickerhamii isolated from the clinic to contribute to the basic understanding of this alga and explore future prevention and treatment strategies. Journal Article Frontiers in Cellular and Infection Microbiology 12 Frontiers Media SA 2235-2988 Prototheca wickerhamii, protothecosis, algae, whole genome sequencing, pathogenic 2 2 2022 2022-02-02 10.3389/fcimb.2022.797017 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University This work was supported by the National Natural Science Foundation [grant number 81971990], Key Discipline of Public Health in Shanghai [grant number GWV-10.1-XK04], Excellent Technology Leader in Shanghai [grant number 20XD1434500], and Novo Nordisk Foundation [grant number NNF20OC0064249]. 2022-11-04T17:53:44.8810832 2022-10-31T12:54:38.2182950 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Jian Guo 1 Jianbo Jian 2 Lili Wang 3 Lijuan Xiong 4 Huiping Lin 5 Ziyi Zhou 6 Eva C. Sonnenschein 0000-0001-6959-5100 7 Wenjuan Wu 8 61715__25659__05d70689f5a5461e9c2581a6aa63c224.pdf 61715.pdf 2022-11-04T17:52:20.2610612 Output 3811453 application/pdf Version of Record true © 2022 Guo, Jian, Wang, Xiong, Lin, Zhou, Sonnenschein and Wu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) true eng http://creativecommons.org/licenses/by/4.0/
title Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
spellingShingle Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
Eva C. Sonnenschein
title_short Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
title_full Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
title_fullStr Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
title_full_unstemmed Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
title_sort Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution
author_id_str_mv f6a4027578a15ea3e6453a54b849c686
author_id_fullname_str_mv f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein
author Eva C. Sonnenschein
author2 Jian Guo
Jianbo Jian
Lili Wang
Lijuan Xiong
Huiping Lin
Ziyi Zhou
Eva C. Sonnenschein
Wenjuan Wu
format Journal article
container_title Frontiers in Cellular and Infection Microbiology
container_volume 12
publishDate 2022
institution Swansea University
issn 2235-2988
doi_str_mv 10.3389/fcimb.2022.797017
publisher Frontiers Media SA
college_str Faculty of Science and Engineering
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hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
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description The Prototheca alga is the only chlorophyte known to be involved in a series of clinically relevant opportunistic infections in humans and animals, namely, protothecosis. Most pathogenic cases in humans are caused by Prototheca wickerhamii. In order to investigate the evolution of Prototheca and the genetic basis for its pathogenicity, the genomes of two P. wickerhamii strains S1 and S931 were sequenced using Nanopore long-read and Illumina short-read technologies. The mitochondrial, plastid, and nuclear genomes were assembled and annotated including a transcriptomic data set. The assembled nuclear genome size was 17.57 Mb with 19 contigs and 17.45 Mb with 26 contigs for strains S1 and S931, respectively. The number of predicted protein-coding genes was approximately 5,700, and more than 96% of the genes could be annotated with a gene function. A total of 2,798 gene families were shared between the five currently available Prototheca genomes. According to the phylogenetic analysis, the genus of Prototheca was classified in the same clade with A. protothecoides and diverged from Chlorella ~500 million years ago (Mya). A total of 134 expanded genes were enriched in several pathways, mostly in metabolic pathways, followed by biosynthesis of secondary metabolites and RNA transport. Comparative analysis demonstrated more than 96% consistency between the two herein sequenced strains. At present, due to the lack of sufficient understanding of the Prototheca biology and pathogenicity, the diagnosis rate of protothecosis is much lower than the actual infection rate. This study provides an in-depth insight into the genome sequences of two strains of P. wickerhamii isolated from the clinic to contribute to the basic understanding of this alga and explore future prevention and treatment strategies.
published_date 2022-02-02T04:20:44Z
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