Genome analysis of sponge symbiont ‘<i>Candidatus</i> Halichondribacter symbioticus’ shows genomic adaptation to a host‐dependent lifestyle

Knobloch, Stephen; Jóhannsson, Ragnar; Marteinsson, V.

doi:10.1111/1462-2920.14869

Cited by 22 publications

(26 citation statements)

References 101 publications

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“…Also present are the genes necessary to biosynthesize valine, leucine, isoleucine, tryptophan, phenylalanine, tyrosine, and ornithine amino acids, as well as genes required for transport of l -amino acids, proline, and branched amino acids. This would suggest that this bacterium may exchange amino acids with the host, as observed previously in both insect and sponge-associated symbioses ( 11 , 65 , 66 ).…”

Section: Resultssupporting

confidence: 64%

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

Waterworth

Parker-Nance

Kwan

et al. 2021

mBio

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Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa ( Entoporibacteria , SAUL , and Tethybacterales ) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two.

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Section: Resultssupporting

confidence: 64%

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

Waterworth

Parker-Nance

Kwan

et al. 2021

mBio

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“…Also present are the genes necessary to biosynthesize valine, leucine, isoleucine, tryptophan, phenylalanine, tyrosine and ornithine amino acids as well as genes required for transport of L-amino acids, proline and branched amino acids. This would suggest that this bacterium may exchange amino acids with the host, as observed previously in both insect and sponge-associated symbioses (8,83,84).…”

Section: Characterization Of Putative Betaproteobacteria Sp02-1 Genome Binsupporting

confidence: 64%

Comparative genomics provides insight into the function of broad-host range sponge symbionts

Waterworth

Parker-Nance

Kwan³

et al. 2020

Preprint

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Sponges have evolved complex associations with conserved bacteria symbionts that contribute to the fitness of the host. Sponges of the family, Latrunculiidae, produce a diverse array of cytotoxic pyrroloiminoquinone alkaloids and their microbiomes are dominated by a conserved spirochete and betaproteobacterium. We investigated the microbiome of Tsitsikamma favus, a latrunculid species that produces predominantly tsitsikammamines. A total of 50 Metagenome-Assembled-Genomes (MAGs) were recovered from the four metagenomes, including representatives of the conserved spirochete and betaproteobacterium symbionts. We predict that the Sp02-3, one of two spirochetes unique to latrunculid species, is likely an anaerobic symbiont that produces vitamin B6. Dysbiosis of the spirochete population correlates with the chemistry associated with distinct sponge chemotypes, implying a role in pyrroloiminoquinone production. The betaproteobacteria symbiont belongs to the newly defined Tethybacterales order and likely aids in the removal of nitrate. There is also evidence to suggest that the two symbionts may work in tandem to remove sulfate from the sponge. Additionally, we analyzed seventeen Tethybacterales genomes and identified a third family within the order. The phylogeny of Tethybacterales is incongruent with that of the sponge hosts suggesting that the association of Tethybacterales and their sponge hosts likely occurred multiple times over their evolutionary history.

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“…The goal was then to use this reference to study changes in gene expression under different oxygen concentrations in order to understand how this species tolerates hypoxia [see 1]. During the process of data collection, Knobloch et al [2] generated a reference genome for the dominant microbial symbiont 'Candidatus Halichondribacter symbioticus', and the data presented here were not sufficient to construct a suitable reference genome for the sponge, limiting the scope of these data for a full research paper.…”

Section: Objectivementioning

confidence: 99%

Metagenomic data for Halichondria panicea from Illumina and Nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts

Strehlow

Schuster

Francis

et al. 2021

Preprint

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Objectives: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses. Data description: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of H. panicea - one Illumina MiSeq (2x300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the best assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3,084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.

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Genome analysis of sponge symbiont ‘Candidatus Halichondribacter symbioticus’ shows genomic adaptation to a host‐dependent lifestyle

Cited by 22 publications

References 101 publications

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

Comparative genomics provides insight into the function of broad-host range sponge symbionts

Metagenomic data for Halichondria panicea from Illumina and Nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts

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