Comparative algal genomics often relies on predicted genes 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 the Symbiodiniaceae, we identified methodological biases in the published genes that were predicted using different approaches and putative contaminant sequences in the published genome assemblies. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted genes resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas the variation among the previously published genes was largely biased by the distinct approaches used in each instance. Importantly, these biases affect 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 analysis of dinoflagellate genomes.

中文翻译：

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不一致的基因预测可能会误导甲藻基因组分析的证据。


比较藻类基因组学通常依赖于从头组装的基因组中预测的基因。然而，不同基因预测方法引入的伪影及其对比较基因组分析的影响仍然知之甚少。在这里，利用共生科中六种甲藻的可用基因组数据，我们确定了已发表基因中的方法学偏差，这些基因是使用不同方法和已发表基因组组装中的假定污染物序列进行预测的。我们开发并应用了全面的定制工作流程来预测这些基因组中的基因。从我们的工作流程中观察到的预测基因之间的变异与当前对这些类群之间系统发育关系的理解一致，而之前发表的基因之间的变异很大程度上是由于每个实例中使用的不同方法而产生的偏差。重要的是，这些偏差影响同源基因家族的推断和基因组之间的同线性，从而影响这些数据的生物学解释。我们的结果表明，一致的基因预测方法对于甲藻基因组的比较分析至关重要。