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Metagenomic analysis of fish-associated Ca. Parilichlamydiaceae reveals striking metabolic similarities to the terrestrial Chlamydiaceae

Citation

Taylor-Brown, A and Pillonel, T and Greub, G and Vaughan, L and Nowak, B and Polkinghorne, A, Metagenomic analysis of fish-associated Ca. Parilichlamydiaceae reveals striking metabolic similarities to the terrestrial Chlamydiaceae, Genome Biology and Evolution, 10, (10) pp. 2614-2628. ISSN 1759-6653 (2018) [Refereed Article]


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Copyright The Author(s) 2018. Licensed under Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) https://creativecommons.org/licenses/by-nc/4.0/

DOI: doi:10.1093/gbe/evy195

Abstract

Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.03.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.

Item Details

Item Type:Refereed Article
Keywords:Chlamydiae, Chlamydia-related bacteria, genomics, metagenomics, convergent evolution, intracellular bacteria, metabolism
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Fisheries sciences
Research Field:Fish pests and diseases
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - aquaculture
Objective Field:Aquaculture fin fish (excl. tuna)
UTAS Author:Nowak, B (Professor Barbara Nowak)
ID Code:129952
Year Published:2018
Web of Science® Times Cited:3
Deposited By:Fisheries and Aquaculture
Deposited On:2019-01-02
Last Modified:2019-03-28
Downloads:49 View Download Statistics

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