MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes
Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the na...
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ftdoajarticles:oai:doaj.org/article:20d5c449149f44be90866e45fe586d26 2023-05-15T17:48:03+02:00 MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes Catherine Maggiori Isabelle Raymond-Bouchard Laura Brennan David Touchette Lyle Whyte 2021-10-01T00:00:00Z https://doi.org/10.1038/s41598-021-00026-x https://doaj.org/article/20d5c449149f44be90866e45fe586d26 EN eng Nature Portfolio https://doi.org/10.1038/s41598-021-00026-x https://doaj.org/toc/2045-2322 doi:10.1038/s41598-021-00026-x 2045-2322 https://doaj.org/article/20d5c449149f44be90866e45fe586d26 Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021) Medicine R Science Q article 2021 ftdoajarticles https://doi.org/10.1038/s41598-021-00026-x 2022-12-31T07:30:48Z Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. Article in Journal/Newspaper Nunavut Sea ice Directory of Open Access Journals: DOAJ Articles Nunavut Allen Bay ENVELOPE(-36.533,-36.533,-54.183,-54.183) Scientific Reports 11 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Catherine Maggiori Isabelle Raymond-Bouchard Laura Brennan David Touchette Lyle Whyte MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
topic_facet |
Medicine R Science Q |
description |
Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. |
format |
Article in Journal/Newspaper |
author |
Catherine Maggiori Isabelle Raymond-Bouchard Laura Brennan David Touchette Lyle Whyte |
author_facet |
Catherine Maggiori Isabelle Raymond-Bouchard Laura Brennan David Touchette Lyle Whyte |
author_sort |
Catherine Maggiori |
title |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_short |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_fullStr |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full_unstemmed |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_sort |
minion sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
publisher |
Nature Portfolio |
publishDate |
2021 |
url |
https://doi.org/10.1038/s41598-021-00026-x https://doaj.org/article/20d5c449149f44be90866e45fe586d26 |
long_lat |
ENVELOPE(-36.533,-36.533,-54.183,-54.183) |
geographic |
Nunavut Allen Bay |
geographic_facet |
Nunavut Allen Bay |
genre |
Nunavut Sea ice |
genre_facet |
Nunavut Sea ice |
op_source |
Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021) |
op_relation |
https://doi.org/10.1038/s41598-021-00026-x https://doaj.org/toc/2045-2322 doi:10.1038/s41598-021-00026-x 2045-2322 https://doaj.org/article/20d5c449149f44be90866e45fe586d26 |
op_doi |
https://doi.org/10.1038/s41598-021-00026-x |
container_title |
Scientific Reports |
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11 |
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1 |
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1766153239590338560 |