Cargando…

Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data

Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicit...

Descripción completa

Detalles Bibliográficos
Autores principales: Sigova, Elizaveta A., Pushkova, Elena N., Rozhmina, Tatiana A., Kudryavtseva, Ludmila P., Zhuchenko, Alexander A., Novakovskiy, Roman O., Zhernova, Daiana A., Povkhova, Liubov V., Turba, Anastasia A., Borkhert, Elena V., Melnikova, Nataliya V., Dmitriev, Alexey A., Dvorianinova, Ekaterina M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055923/
https://www.ncbi.nlm.nih.gov/pubmed/36983469
http://dx.doi.org/10.3390/jof9030301
_version_ 1785015998038933504
author Sigova, Elizaveta A.
Pushkova, Elena N.
Rozhmina, Tatiana A.
Kudryavtseva, Ludmila P.
Zhuchenko, Alexander A.
Novakovskiy, Roman O.
Zhernova, Daiana A.
Povkhova, Liubov V.
Turba, Anastasia A.
Borkhert, Elena V.
Melnikova, Nataliya V.
Dmitriev, Alexey A.
Dvorianinova, Ekaterina M.
author_facet Sigova, Elizaveta A.
Pushkova, Elena N.
Rozhmina, Tatiana A.
Kudryavtseva, Ludmila P.
Zhuchenko, Alexander A.
Novakovskiy, Roman O.
Zhernova, Daiana A.
Povkhova, Liubov V.
Turba, Anastasia A.
Borkhert, Elena V.
Melnikova, Nataliya V.
Dmitriev, Alexey A.
Dvorianinova, Ekaterina M.
author_sort Sigova, Elizaveta A.
collection PubMed
description Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases.
format Online
Article
Text
id pubmed-10055923
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-100559232023-03-30 Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data Sigova, Elizaveta A. Pushkova, Elena N. Rozhmina, Tatiana A. Kudryavtseva, Ludmila P. Zhuchenko, Alexander A. Novakovskiy, Roman O. Zhernova, Daiana A. Povkhova, Liubov V. Turba, Anastasia A. Borkhert, Elena V. Melnikova, Nataliya V. Dmitriev, Alexey A. Dvorianinova, Ekaterina M. J Fungi (Basel) Article Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases. MDPI 2023-02-26 /pmc/articles/PMC10055923/ /pubmed/36983469 http://dx.doi.org/10.3390/jof9030301 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sigova, Elizaveta A.
Pushkova, Elena N.
Rozhmina, Tatiana A.
Kudryavtseva, Ludmila P.
Zhuchenko, Alexander A.
Novakovskiy, Roman O.
Zhernova, Daiana A.
Povkhova, Liubov V.
Turba, Anastasia A.
Borkhert, Elena V.
Melnikova, Nataliya V.
Dmitriev, Alexey A.
Dvorianinova, Ekaterina M.
Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title_full Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title_fullStr Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title_full_unstemmed Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title_short Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
title_sort assembling quality genomes of flax fungal pathogens from oxford nanopore technologies data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055923/
https://www.ncbi.nlm.nih.gov/pubmed/36983469
http://dx.doi.org/10.3390/jof9030301
work_keys_str_mv AT sigovaelizavetaa assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT pushkovaelenan assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT rozhminatatianaa assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT kudryavtsevaludmilap assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT zhuchenkoalexandera assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT novakovskiyromano assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT zhernovadaianaa assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT povkhovaliubovv assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT turbaanastasiaa assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT borkhertelenav assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT melnikovanataliyav assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT dmitrievalexeya assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata
AT dvorianinovaekaterinam assemblingqualitygenomesofflaxfungalpathogensfromoxfordnanoporetechnologiesdata