ArticleScientific reports2023
Addressing the pervasive scarcity of structural annotation in eukaryotic algae.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.
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Who cites it
10 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.Environmental microbiology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- Nuclear genome assembly and annotation for the phagotrophic green alga Nephroselmis pyriformis.Journal of phycology · 2025Article
- Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella.The Plant cell · 2025Article
- Targeted genetic manipulation and yeast-like evolutionary genomics in the green algabioRxiv : the preprint server for biology · 2025Article
- An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.Bioinformatics advances · 2025Review
- Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures.Scientific reports · 2024Article
- Comparative Genomic Analysis of aInternational journal of molecular sciences · 2023Article
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3 authors.
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No grant is acknowledged in the PubMed record.
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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