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://doi.org/10.3390/md21030165 |
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ftmdpi:oai:mdpi.com:/1660-3397/21/3/165/ 2023-08-20T04:04:17+02:00 Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates Andrea Iselin Elvheim Chun Li Bjarne Landfald agris 2023-03-02 application/pdf https://doi.org/10.3390/md21030165 EN eng Multidisciplinary Digital Publishing Institute https://dx.doi.org/10.3390/md21030165 https://creativecommons.org/licenses/by/4.0/ Marine Drugs; Volume 21; Issue 3; Pages: 165 marine invertebrates microbiomes multiple displacement amplification metagenomics biosynthetic gene clusters Text 2023 ftmdpi https://doi.org/10.3390/md21030165 2023-08-01T09:05:02Z 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. Text Arctic MDPI Open Access Publishing Arctic Marine Drugs 21 3 165 |
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Open Polar |
collection |
MDPI Open Access Publishing |
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ftmdpi |
language |
English |
topic |
marine invertebrates microbiomes multiple displacement amplification metagenomics biosynthetic gene clusters |
spellingShingle |
marine invertebrates microbiomes multiple displacement amplification metagenomics biosynthetic gene clusters Andrea Iselin Elvheim Chun Li Bjarne Landfald Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates |
topic_facet |
marine invertebrates microbiomes multiple displacement amplification metagenomics biosynthetic gene clusters |
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 |
Text |
author |
Andrea Iselin Elvheim Chun Li Bjarne Landfald |
author_facet |
Andrea Iselin Elvheim Chun Li Bjarne Landfald |
author_sort |
Andrea Iselin Elvheim |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2023 |
url |
https://doi.org/10.3390/md21030165 |
op_coverage |
agris |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Marine Drugs; Volume 21; Issue 3; Pages: 165 |
op_relation |
https://dx.doi.org/10.3390/md21030165 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/md21030165 |
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Marine Drugs |
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