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Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).
Am J Bot. 2018 03; 105(3):330-347.AJ

Abstract

PREMISE OF THE STUDY

Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well.

METHODS

We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species.

KEY RESULTS

Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.

CONCLUSIONS

Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.

Authors+Show Affiliations

Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL, 60022, USA.Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA.Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA.Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL, 60022, USA.Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

29665021

Citation

Parks, Matthew B., et al. "Phylogenomics Reveals an Extensive History of Genome Duplication in Diatoms (Bacillariophyta)." American Journal of Botany, vol. 105, no. 3, 2018, pp. 330-347.
Parks MB, Nakov T, Ruck EC, et al. Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). Am J Bot. 2018;105(3):330-347.
Parks, M. B., Nakov, T., Ruck, E. C., Wickett, N. J., & Alverson, A. J. (2018). Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). American Journal of Botany, 105(3), 330-347. https://doi.org/10.1002/ajb2.1056
Parks MB, et al. Phylogenomics Reveals an Extensive History of Genome Duplication in Diatoms (Bacillariophyta). Am J Bot. 2018;105(3):330-347. PubMed PMID: 29665021.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). AU - Parks,Matthew B, AU - Nakov,Teofil, AU - Ruck,Elizabeth C, AU - Wickett,Norman J, AU - Alverson,Andrew J, Y1 - 2018/04/17/ PY - 2017/08/25/received PY - 2017/12/18/accepted PY - 2018/4/18/pubmed PY - 2019/3/1/medline PY - 2018/4/18/entrez KW - diatoms KW - gene tree KW - genome duplication KW - paleopolyploidy KW - polyploidy KW - synonymous divergence SP - 330 EP - 347 JF - American journal of botany JO - Am. J. Bot. VL - 105 IS - 3 N2 - PREMISE OF THE STUDY: Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. METHODS: We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. KEY RESULTS: Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. CONCLUSIONS: Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity. SN - 1537-2197 UR - https://www.unboundmedicine.com/medline/citation/29665021/Phylogenomics_reveals_an_extensive_history_of_genome_duplication_in_diatoms__Bacillariophyta__ L2 - https://doi.org/10.1002/ajb2.1056 DB - PRIME DP - Unbound Medicine ER -