Addressing the pervasive scarcity of structural annotation in eukaryotic algae

Kwon, Taehyung; Hanschen, Erik R.; Hovde, Blake T.

doi:10.1038/s41598-023-27881-0

Addressing the pervasive scarcity of structural annotation in eukaryotic algae

Journal Article · Mon Jan 30 00:00:00 EST 2023 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-023-27881-0· OSTI ID:1922580

Kwon, Taehyung; Hanschen, Erik R.; Hovde, Blake T.

Abstract

Despite a continuous increase in algal genome sequencing, structural annotations of most algal genome assemblies remain unavailable. This pervasive scarcity of genome annotation has restricted rigorous investigation of these genomic resources and may have precipitated misleading biological interpretations. However, the annotation process for eukaryotic algal species is often challenging as genomic resources and transcriptomic evidence are not always available. To address this challenge, we benchmark the cutting-edge gene prediction methods that can be generalized for a broad range of non-model eukaryotes. Using the most accurate methods selected based on high-quality algal genomes, we predict structural annotations for 135 unannotated algal genomes. Using previously available genomic data pooled together with new data obtained in this study, we identified the core orthologous genes and the multi-gene phylogeny of eukaryotic algae, including of previously unexplored algal species. This study not only provides a benchmark for the use of structural annotation methods on a variety of non-model eukaryotes, but also compensates for missing data in the current spectrum of algal genomic resources. These results bring us one step closer to the full potential of eukaryotic algal genomics.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC)

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 1922580

Alternate ID(s):: OSTI ID: 1924408

Report Number(s):: LA-UR-21-30119; 1687; PII: 27881

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 13; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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