Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However,...
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Online Access: | https://hdl.handle.net/10037/30128 https://doi.org/10.3390/md21030165 |
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ftunivtroemsoe:oai:munin.uit.no:10037/30128 2023-09-05T13:17:09+02:00 Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates Elvheim, Andrea Iselin Li, Chun Landfald, Bjarne 2023-03-02 https://hdl.handle.net/10037/30128 https://doi.org/10.3390/md21030165 eng eng MDPI Marine Drugs Elvheim, Li, Landfald. Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Marine Drugs. 2023;21(3) FRIDAID 2141395 doi:10.3390/md21030165 1660-3397 https://hdl.handle.net/10037/30128 Attribution 4.0 International (CC BY 4.0) openAccess Copyright 2023 The Author(s) https://creativecommons.org/licenses/by/4.0 Journal article Tidsskriftartikkel Peer reviewed publishedVersion 2023 ftunivtroemsoe https://doi.org/10.3390/md21030165 2023-08-23T23:07:11Z Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources. Article in Journal/Newspaper Arctic University of Tromsø: Munin Open Research Archive Arctic Marine Drugs 21 3 165 |
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Open Polar |
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University of Tromsø: Munin Open Research Archive |
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ftunivtroemsoe |
language |
English |
description |
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources. |
format |
Article in Journal/Newspaper |
author |
Elvheim, Andrea Iselin Li, Chun Landfald, Bjarne |
spellingShingle |
Elvheim, Andrea Iselin Li, Chun Landfald, Bjarne Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
author_facet |
Elvheim, Andrea Iselin Li, Chun Landfald, Bjarne |
author_sort |
Elvheim, Andrea Iselin |
title |
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
title_short |
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
title_full |
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
title_fullStr |
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
title_full_unstemmed |
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
title_sort |
conservation of genomic information in multiple displacement amplified low-quantity metagenomic material from marine invertebrates |
publisher |
MDPI |
publishDate |
2023 |
url |
https://hdl.handle.net/10037/30128 https://doi.org/10.3390/md21030165 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
Marine Drugs Elvheim, Li, Landfald. Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Marine Drugs. 2023;21(3) FRIDAID 2141395 doi:10.3390/md21030165 1660-3397 https://hdl.handle.net/10037/30128 |
op_rights |
Attribution 4.0 International (CC BY 4.0) openAccess Copyright 2023 The Author(s) https://creativecommons.org/licenses/by/4.0 |
op_doi |
https://doi.org/10.3390/md21030165 |
container_title |
Marine Drugs |
container_volume |
21 |
container_issue |
3 |
container_start_page |
165 |
_version_ |
1776198439287128064 |