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Taxonomy of the genus Serratia

Student:

Ekaterina Sukhinina

Supervisors:

Kirill Antonets

Anton Shikov

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Introduction

In 2020 two new species of the genus Serratia were identified – S. nevei and S. bockelmannii.

New species were identified using biochemical and morphological characteristics and a phylogenetic tree based on limited genome set. Many genomes previously labeled as S. marcescens may belong to these new species not yet recognized by taxonomists and listed as unvalidated in NCBI database.

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Aim and objectives

Aim: to investigate whether the subdivision into species of the genus Serratia is consistent with the actual phylogeny

Objectives:

Download the Serratia genomes from the NCBI Assembly database
Reconstruct the phylogeny of the genus based on the distance matrix between genomes.
Perform core gene alignment and obtain core SNPs.
Identify suitable models of evolution for phylogenetic analysis.
Reconstruct the genus phylogeny based on core gene alignment and the optimal evolutionary model.

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Methods

Compute a distance matrix between genomic assemblies

Sourmash

(Titus Brown and Irber, 2015)

Reconstruct a phylogenetic tree based on the distance matrix

Obtain core gene alignment and reconstruct pangenome

Remove recombination events from the alignment

Obtain core SNPs

Determine the optimal substitution model

ClonalFrameML

(Didelot and Wilson, 2015)

SNP-sites

(Page, 2016)

Hclust

(R Core Team, 2013)

ModelTest-NG

(Darriba, 2020)

Build a phylogenetic tree

RAxML-NG

(Kozlov, 2019)

Determine the taxonomic assignment of the branches

ggtree (Yu, 2017)

Determine the taxonomic assignment of the branches

ggtree (Yu, 2017)

Panaroo

(Tonkin-Hill, 2020)

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Results

Phylogenetic tree of the genus Serratia based on core gene alignment. NCBI declared and best-match Serratia species are highlighted in the tree's color scheme. Type strains are marked with a diamond.

S. marcescens assemblies, which has not been taxonomically verified by the NCBI, is taxonomically reassigned to the Serratia nevei isolated in 2020.

Serratia bockelmannii is not a separate species and can be considered as S. marcescens

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Future plans

Removing recombinations reduced the size of the alignment more than the actual size of the recombination events. Because we performed the analysis within the genus, local similarities between individual species were perceived as recombination events. It is reasonable to reprocess the data without performing this step.