Microbial phylogenetic context using phylogenetic outlines

Bagci, Caner and Bryant, David and Çetinkaya, Banu and Huson, Daniel H. (2021) Microbial phylogenetic context using phylogenetic outlines. Genome Biology and Evolution, 13 (9). ISSN 1759-6653

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Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes. We provide a new interactive graphical tool that addresses this task using Mash sketches to compare against all bacterial and archaeal representative genomes in the Genome Taxonomy Database taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic network that is more general than a phylogenetic tree, but significantly less complex than other types of phylogenetic networks. We propose to use such networks, rather than trees, to represent phylogenetic context, because they can express uncertainty in the placement of taxa, whereas a tree must always commit to a specific branching pattern. We illustrate the new method using a number of draft genomes of different assembly quality.
Item Type: Article
Uncontrolled Keywords: algorithms; genomes; k-mers; phylogenetic networks; phylogeny; software
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Computer Science & Eng.
Faculty of Engineering and Natural Sciences
Depositing User: Banu Çetinkaya
Date Deposited: 28 Aug 2022 10:31
Last Modified: 28 Aug 2022 10:31
URI: https://research.sabanciuniv.edu/id/eprint/43821

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