Predicting stop codon reassignment improves functional annotation of bacteriophages
Predicting stop codon reassignment improves functional annotation of bacteriophages
复制标题
预测终止密码子重新分配可改善噬菌体的功能注释
DOI：
10.1101/2023.12.19.572299
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Cook R
中科院分区：
文献类型：
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作者：
Cook R
大多数噬菌体的多样性仍然没有被描述，它们生物学的新的有趣机制正在不断被描述。一些噬菌体谱系的成员，如粗病毒目，通过使用替代遗传密码来重新利用终止密码子来编码氨基酸。在这里，我们调查了终止密码子重新分配在噬菌体基因组中的流行率和随后对功能注释的影响。我们预测了INPHARED中的76个基因组和来自统一人类肠道病毒目录（UHGV）的712个vOTU，这些基因组重新使用终止密码子来编码氨基酸。我们用Pharokka和Prokka的修改版本（称为Pharokka-gv和Prokka-gv）重新注释了这些序列，以在注释之前自动预测终止密码子的重新分配。这两个工具都显著提高了注释的质量，其中Pharokka-gv表现最好。对于预测将TAG重新用于谷氨酰胺的序列（翻译表15），Pharokka-gv将UHGV序列的中位基因长度（每个基因组中位数的中位数）从287增加到481 bp（增加67.8%），将INPHARED序列的中位基因长度从318增加到550 bp（增加72.9%）。重新注释使UHGV和INPHARED序列的平均编码密度从66.8%增加到90.0%，从69.0%增加到89.8%。此外，可以分配功能注释的基因的比例增加，包括可以鉴定的主要衣壳蛋白的数量增加。我们建议在注释之前自动预测终止密码子的重新分配，这对下游病毒基因组和宏基因组分析是有益的。
The majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome medians) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased mean coding density from 66.8% to 90.0%, and from 69.0% to 89.8% for UHGV and INPHARED sequences. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.