Genomics and Bioanalytics, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Sci Rep. 2023 Jan 30;13(1):1687. doi: 10.1038/s41598-023-27881-0.
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.
尽管藻类基因组测序不断增加，但大多数藻类基因组组装的结构注释仍然不可用。这种普遍缺乏基因组注释的情况限制了对这些基因组资源的严格研究，并可能导致了误导性的生物学解释。然而，真核藻类物种的注释过程通常具有挑战性，因为基因组资源和转录组证据并不总是可用。为了解决这一挑战，我们对可广泛应用于多种非模式真核生物的最先进的基因预测方法进行了基准测试。我们使用基于高质量藻类基因组选择的最准确方法，为 135 个未注释的藻类基因组预测结构注释。利用以前可用的基因组数据和本研究中获得的新数据，我们确定了真核藻类的核心直系同源基因和多基因系统发育，包括以前未探索的藻类物种。这项研究不仅为在各种非模式真核生物上使用结构注释方法提供了基准，还弥补了当前藻类基因组资源谱中缺失的数据。这些结果使我们更接近真核藻类基因组学的全部潜力。
