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Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum

Jianbo Jian, Zhangyan Wu, Arisbe Silva-Núñez, Xiaohui Li, Xiaomin Zheng, Bei Luo, Yun Liu, Xiaodong Fang, Christopher T. Workman, Thomas Ostenfeld Larsen, Per Juel Hansen, Eva C. Sonnenschein Orcid Logo

Science of The Total Environment, Volume: 908, Start page: 168042

Swansea University Author: Eva C. Sonnenschein Orcid Logo

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DOI (Published version): 10.1016/j.scitotenv.2023.168042

Abstract

Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P...

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Published in: Science of The Total Environment
ISSN: 0048-9697 1879-1026
Published: Elsevier BV 2024
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URI: https://cronfa.swan.ac.uk/Record/cronfa64836
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In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. 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spelling v2 64836 2023-10-30 Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2023-10-30 SBI Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future. Journal Article Science of The Total Environment 908 168042 Elsevier BV 0048-9697 1879-1026 Harmful algal blooms, Comparative genomics, Horizontal gene transfer, Polyketide synthase 15 1 2024 2024-01-15 10.1016/j.scitotenv.2023.168042 http://dx.doi.org/10.1016/j.scitotenv.2023.168042 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University SU Library paid the OA fee (TA Institutional Deal) Swansea University 2023-11-15T09:45:36.6787373 2023-10-30T10:33:44.3403851 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Jianbo Jian 1 Zhangyan Wu 2 Arisbe Silva-Núñez 3 Xiaohui Li 4 Xiaomin Zheng 5 Bei Luo 6 Yun Liu 7 Xiaodong Fang 8 Christopher T. Workman 9 Thomas Ostenfeld Larsen 10 Per Juel Hansen 11 Eva C. Sonnenschein 0000-0001-6959-5100 12 64836__29025__e006e9fbc58844e5974fee1e86e24a5c.pdf 64836.VOR.pdf 2023-11-15T09:42:15.9775481 Output 10194247 application/pdf Version of Record true © 2023 The Authors. Published by Elsevier B.V. Distributed under the terms of a Creative Commons Attribution 4.0 International License (CC BY 4.0). true eng https://creativecommons.org/licenses/by/4.0/
title Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
spellingShingle Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
Eva C. Sonnenschein
title_short Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
title_full Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
title_fullStr Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
title_full_unstemmed Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
title_sort Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
author_id_str_mv f6a4027578a15ea3e6453a54b849c686
author_id_fullname_str_mv f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein
author Eva C. Sonnenschein
author2 Jianbo Jian
Zhangyan Wu
Arisbe Silva-Núñez
Xiaohui Li
Xiaomin Zheng
Bei Luo
Yun Liu
Xiaodong Fang
Christopher T. Workman
Thomas Ostenfeld Larsen
Per Juel Hansen
Eva C. Sonnenschein
format Journal article
container_title Science of The Total Environment
container_volume 908
container_start_page 168042
publishDate 2024
institution Swansea University
issn 0048-9697
1879-1026
doi_str_mv 10.1016/j.scitotenv.2023.168042
publisher Elsevier BV
college_str Faculty of Science and Engineering
hierarchytype
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
url http://dx.doi.org/10.1016/j.scitotenv.2023.168042
document_store_str 1
active_str 0
description Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
published_date 2024-01-15T09:45:39Z
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