Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts
Abstract
Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
Additional Information
© 2021 John Wiley & Sons Ltd. Issue Online: 23 July 2021; Version of Record online: 28 May 2021; Accepted manuscript online: 08 May 2021; Manuscript accepted: 04 May 2021; Manuscript revised: 01 May 2021; Manuscript received: 07 October 2020. Data Availability Statement: Sequences are available under NCBI SRA PRJNA473816. Code for data analysis and figure generation is available on github (https://github.com/hgreich/Sfitti). The draft genome assembly for the reference A. cervicornis–S. 'fitti' is available on dryad https://doi.org/10.5061/dryad.xgxd254g8. Research Funding: National Science Foundation. Grant Numbers: 1537959, 1538469, 1929979Attached Files
Supplemental Material - mec15952-sup-0001-figs1-s6.pdf
Supplemental Material - mec15952-sup-0002-tables1-s10.xlsx
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Additional details
- Eprint ID
- 109039
- Resolver ID
- CaltechAUTHORS:20210510-140117824
- OCE-1537959
- NSF
- OCE-1538469
- NSF
- OCE-1929979
- NSF
- Created
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2021-05-10Created from EPrint's datestamp field
- Updated
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2021-08-11Created from EPrint's last_modified field