A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome
ABSTRACT Current supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from under-investigated habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, “Genome Constellation”, that estimate...
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ftcdlib:oai:escholarship.org:ark:/13030/qt5jx0c4hg 2023-09-05T13:14:11+02:00 A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome Wang, Zhong Ho, Harrison Egan, Rob Yao, Shijie Kang, Dongwan Froula, Jeff Sevim, Volkan Schulz, Frederik Shay, Jackie Macklin, Derek McCue, Kayla Orsini, Rachel Barich, Daniel Sedlacek, Christopher Li, Wei Morgan-Kiss, Rachael Woyke, Tanja Slonczewski, Joan 2019-01-01 application/pdf https://escholarship.org/uc/item/5jx0c4hg unknown eScholarship, University of California qt5jx0c4hg https://escholarship.org/uc/item/5jx0c4hg public Genetics Networking and Information Technology R&D (NITRD) Human Genome article 2019 ftcdlib 2023-08-14T18:05:06Z ABSTRACT Current supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from under-investigated habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, “Genome Constellation”, that estimates similarities between genomes based on their k-mer matches, and subsequently uses these similarities for classification, clustering, and visualization. The clusters of reference genomes formed by Genome Constellation closely resemble known phylogenetic relationships while simultaneously revealing unexpected connections. In a dataset containing 1,693 draft genomes assembled from the Antarctic lake communities where only 40% could be placed in a phylogenetic tree, Genome Constellation improves taxa assignment to 61%. It revealed six clusters derived from new bacterial phyla and 63 new giant viruses, 3 of which missed by the traditional marker-based approach. In summary, we demonstrate that Genome Constellation can tackle the computational and algorithmic challenges in large-scale taxonomy analyses in metagenomics. Article in Journal/Newspaper Antarc* Antarctic University of California: eScholarship Antarctic The Antarctic |
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Open Polar |
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University of California: eScholarship |
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language |
unknown |
topic |
Genetics Networking and Information Technology R&D (NITRD) Human Genome |
spellingShingle |
Genetics Networking and Information Technology R&D (NITRD) Human Genome Wang, Zhong Ho, Harrison Egan, Rob Yao, Shijie Kang, Dongwan Froula, Jeff Sevim, Volkan Schulz, Frederik Shay, Jackie Macklin, Derek McCue, Kayla Orsini, Rachel Barich, Daniel Sedlacek, Christopher Li, Wei Morgan-Kiss, Rachael Woyke, Tanja Slonczewski, Joan A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
topic_facet |
Genetics Networking and Information Technology R&D (NITRD) Human Genome |
description |
ABSTRACT Current supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from under-investigated habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, “Genome Constellation”, that estimates similarities between genomes based on their k-mer matches, and subsequently uses these similarities for classification, clustering, and visualization. The clusters of reference genomes formed by Genome Constellation closely resemble known phylogenetic relationships while simultaneously revealing unexpected connections. In a dataset containing 1,693 draft genomes assembled from the Antarctic lake communities where only 40% could be placed in a phylogenetic tree, Genome Constellation improves taxa assignment to 61%. It revealed six clusters derived from new bacterial phyla and 63 new giant viruses, 3 of which missed by the traditional marker-based approach. In summary, we demonstrate that Genome Constellation can tackle the computational and algorithmic challenges in large-scale taxonomy analyses in metagenomics. |
format |
Article in Journal/Newspaper |
author |
Wang, Zhong Ho, Harrison Egan, Rob Yao, Shijie Kang, Dongwan Froula, Jeff Sevim, Volkan Schulz, Frederik Shay, Jackie Macklin, Derek McCue, Kayla Orsini, Rachel Barich, Daniel Sedlacek, Christopher Li, Wei Morgan-Kiss, Rachael Woyke, Tanja Slonczewski, Joan |
author_facet |
Wang, Zhong Ho, Harrison Egan, Rob Yao, Shijie Kang, Dongwan Froula, Jeff Sevim, Volkan Schulz, Frederik Shay, Jackie Macklin, Derek McCue, Kayla Orsini, Rachel Barich, Daniel Sedlacek, Christopher Li, Wei Morgan-Kiss, Rachael Woyke, Tanja Slonczewski, Joan |
author_sort |
Wang, Zhong |
title |
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
title_short |
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
title_full |
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
title_fullStr |
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
title_full_unstemmed |
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
title_sort |
new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome |
publisher |
eScholarship, University of California |
publishDate |
2019 |
url |
https://escholarship.org/uc/item/5jx0c4hg |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
qt5jx0c4hg https://escholarship.org/uc/item/5jx0c4hg |
op_rights |
public |
_version_ |
1776205227456724992 |