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Evidence that inconsistent gene prediction can mislead analysis of algal genomes

Yibi Chen, View ORCID ProfileRaúl A. González-Pech, View ORCID ProfileTimothy G. Stephens, View ORCID ProfileDebashish Bhattacharya, View ORCID ProfileCheong Xin Chan
doi: https://doi.org/10.1101/690040
Yibi Chen
aInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
bSchool of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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Raúl A. González-Pech
aInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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Timothy G. Stephens
aInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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Debashish Bhattacharya
cDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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Cheong Xin Chan
aInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
bSchool of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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  • For correspondence: c.chan1@uq.edu.au
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Abstract

Comparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.

Footnotes

  • Analysis of Fugacium kawagutii genes revised; order of authorship revised; Figures 1 and 2 revised; Figure S1 and Table S1 updated.

  • https://cloudstor.aarnet.edu.au/plus/s/JXALPndBKLNYgF9

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 22, 2019.
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Evidence that inconsistent gene prediction can mislead analysis of algal genomes
Yibi Chen, Raúl A. González-Pech, Timothy G. Stephens, Debashish Bhattacharya, Cheong Xin Chan
bioRxiv 690040; doi: https://doi.org/10.1101/690040
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Evidence that inconsistent gene prediction can mislead analysis of algal genomes
Yibi Chen, Raúl A. González-Pech, Timothy G. Stephens, Debashish Bhattacharya, Cheong Xin Chan
bioRxiv 690040; doi: https://doi.org/10.1101/690040

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