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Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline

Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis, Tariq Butt Orcid Logo

BMC Genomics, Volume: 22, Issue: 1

Swansea University Author: Tariq Butt Orcid Logo

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DOI (Published version): 10.1186/s12864-021-07390-y

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BackgroundMore accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate...

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Published in: BMC Genomics
ISSN: 1471-2164
Published: Springer Science and Business Media LLC 2021
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URI: https://cronfa.swan.ac.uk/Record/cronfa57538
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Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-generation sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently. In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum.ResultsThe improved assembly allowed for better ab initio gene prediction and a more BUSCO complete proteome set has been generated in comparison to the eight current NCBI reference Metarhizium spp. genomes. Remarkably, we note that including the mitogenome in ab initio gene prediction training improved overall gene prediction. The assembly was further validated by comparing contig assembly agreement across various assemblers, assessing the assembly performance of each tool. Genomic synteny and orthologous protein clusters were compared between Metarhizium brunneum and three other Hypocreales species with complete genomes, identifying core proteins, and listing orthologous protein clusters shared uniquely between the two entomopathogenic fungal species, so as to further facilitate the understanding of molecular mechanisms underpinning fungal-insect pathogenesis.ConclusionsThe novel assembly pipeline may be used for other haploid fungal species, facilitating the need to produce high-quality reference fungal genomes, leading to better understanding of fungal genomic evolution, chromosome structuring and gene regulation.</abstract><type>Journal Article</type><journal>BMC Genomics</journal><volume>22</volume><journalNumber>1</journalNumber><paginationStart/><paginationEnd/><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint/><issnElectronic>1471-2164</issnElectronic><keywords>Metarhizium, Fungi, Genome, Nanopore, Long-read, WGS, Hypocreales</keywords><publishedDay>28</publishedDay><publishedMonth>1</publishedMonth><publishedYear>2021</publishedYear><publishedDate>2021-01-28</publishedDate><doi>10.1186/s12864-021-07390-y</doi><url/><notes/><college>COLLEGE NANME</college><department>Biosciences Geography and Physics School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>BGPS</DepartmentCode><institution>Swansea University</institution><apcterm>Other</apcterm><funders>Grant funding was secured from the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Economic and Social Research Council, the Forestry Commission, the Natural Environment Research Council and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative.</funders><lastEdited>2021-09-08T15:05:52.2122427</lastEdited><Created>2021-08-05T15:14:25.1741296</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Biosciences, Geography and Physics - Biosciences</level></path><authors><author><firstname>Zack</firstname><surname>Saud</surname><order>1</order></author><author><firstname>Alexandra M.</firstname><surname>Kortsinoglou</surname><order>2</order></author><author><firstname>Vassili N.</firstname><surname>Kouvelis</surname><order>3</order></author><author><firstname>Tariq</firstname><surname>Butt</surname><orcid>0000-0002-8789-9543</orcid><order>4</order></author></authors><documents><document><filename>57538__20561__f914f68fa08a4069acb5daad95b1dbd1.pdf</filename><originalFilename>57538.pdf</originalFilename><uploaded>2021-08-05T15:16:18.1991899</uploaded><type>Output</type><contentLength>1727468</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>&#xA9; The Author(s). 2021 This article is licensed under a Creative Commons Attribution 4.0 International License</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>http://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling 2021-09-08T15:05:52.2122427 v2 57538 2021-08-05 Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline 85d1c2ddde272a1176e74978e25ebece 0000-0002-8789-9543 Tariq Butt Tariq Butt true false 2021-08-05 BGPS BackgroundMore accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-generation sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently. In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum.ResultsThe improved assembly allowed for better ab initio gene prediction and a more BUSCO complete proteome set has been generated in comparison to the eight current NCBI reference Metarhizium spp. genomes. Remarkably, we note that including the mitogenome in ab initio gene prediction training improved overall gene prediction. The assembly was further validated by comparing contig assembly agreement across various assemblers, assessing the assembly performance of each tool. Genomic synteny and orthologous protein clusters were compared between Metarhizium brunneum and three other Hypocreales species with complete genomes, identifying core proteins, and listing orthologous protein clusters shared uniquely between the two entomopathogenic fungal species, so as to further facilitate the understanding of molecular mechanisms underpinning fungal-insect pathogenesis.ConclusionsThe novel assembly pipeline may be used for other haploid fungal species, facilitating the need to produce high-quality reference fungal genomes, leading to better understanding of fungal genomic evolution, chromosome structuring and gene regulation. Journal Article BMC Genomics 22 1 Springer Science and Business Media LLC 1471-2164 Metarhizium, Fungi, Genome, Nanopore, Long-read, WGS, Hypocreales 28 1 2021 2021-01-28 10.1186/s12864-021-07390-y COLLEGE NANME Biosciences Geography and Physics School COLLEGE CODE BGPS Swansea University Other Grant funding was secured from the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Economic and Social Research Council, the Forestry Commission, the Natural Environment Research Council and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. 2021-09-08T15:05:52.2122427 2021-08-05T15:14:25.1741296 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Zack Saud 1 Alexandra M. Kortsinoglou 2 Vassili N. Kouvelis 3 Tariq Butt 0000-0002-8789-9543 4 57538__20561__f914f68fa08a4069acb5daad95b1dbd1.pdf 57538.pdf 2021-08-05T15:16:18.1991899 Output 1727468 application/pdf Version of Record true © The Author(s). 2021 This article is licensed under a Creative Commons Attribution 4.0 International License true eng http://creativecommons.org/licenses/by/4.0/
title Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
spellingShingle Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
Tariq Butt
title_short Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
title_full Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
title_fullStr Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
title_full_unstemmed Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
title_sort Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
author_id_str_mv 85d1c2ddde272a1176e74978e25ebece
author_id_fullname_str_mv 85d1c2ddde272a1176e74978e25ebece_***_Tariq Butt
author Tariq Butt
author2 Zack Saud
Alexandra M. Kortsinoglou
Vassili N. Kouvelis
Tariq Butt
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container_title BMC Genomics
container_volume 22
container_issue 1
publishDate 2021
institution Swansea University
issn 1471-2164
doi_str_mv 10.1186/s12864-021-07390-y
publisher Springer Science and Business Media LLC
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
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description BackgroundMore accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-generation sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently. In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum.ResultsThe improved assembly allowed for better ab initio gene prediction and a more BUSCO complete proteome set has been generated in comparison to the eight current NCBI reference Metarhizium spp. genomes. Remarkably, we note that including the mitogenome in ab initio gene prediction training improved overall gene prediction. The assembly was further validated by comparing contig assembly agreement across various assemblers, assessing the assembly performance of each tool. Genomic synteny and orthologous protein clusters were compared between Metarhizium brunneum and three other Hypocreales species with complete genomes, identifying core proteins, and listing orthologous protein clusters shared uniquely between the two entomopathogenic fungal species, so as to further facilitate the understanding of molecular mechanisms underpinning fungal-insect pathogenesis.ConclusionsThe novel assembly pipeline may be used for other haploid fungal species, facilitating the need to produce high-quality reference fungal genomes, leading to better understanding of fungal genomic evolution, chromosome structuring and gene regulation.
published_date 2021-01-28T02:20:02Z
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