Serratia marcescens are gram-negative bacteria found in several environmental niches, including the plant rhizosphere and patients in hospitals. Here, we present the genome of Serratia marcescens strain N4-5 (=NRRL B-65519), which has a size of 5,074,473 bp (664-fold coverage) and contains 4840 protein coding genes, 21 RNA genes, and an average G + C content of 59.7%. N4-5 harbours a plasmid of 11,089 bp and 43.5% G + C content that encodes six unique CDS repeated 2.5× times totalling 13 CDS. Our genome assembly and manual curation uncovered the insertion of two extra copies of the 5S rRNA gene in the assembled sequence, which was confirmed by PCR and Sanger sequencing to be a misassembly. This artefact was subsequently removed from the final assembly. The occurrence of extra copies of the 5S rRNA gene was also observed in most complete genomes of Serratia spp. deposited in public databases in our comparative analysis. These elements, which also occur naturally, can easily be confused with true genetic variation. Efforts to discover and correct assembly artefacts should be made in order to generate genome sequences that represent the biological truth underlying the studied organism. We present the genome of N4-5 and discuss genes potentially involved in biological control activity against plant pathogens and also the possible mechanisms responsible for the artefact we observed in our initial assembly. This report raises awareness about the extra copies of the 5S rRNA gene in sequenced bacterial genomes as they may represent misassemblies and therefore should be verified experimentally.

中文翻译：

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生物防治剂粘质沙雷氏菌 N4-5 菌株的完整基因组序列揭示了组装人工制品

粘质沙雷氏菌是在几个环境生态位中发现的革兰氏阴性细菌，包括植物根际和医院的患者。在这里，我们展示了粘质沙雷氏菌 N4-5 (=NRRL B-65519) 的基因组，其大小为 5,074,473 bp（664 倍覆盖），包含 4840 个蛋白质编码基因、21 个 RNA 基因和平均 G + C含量59.7%。N4-5 包含一个 11,089 bp 和 43.5% G + C 含量的质粒，它编码六个独特的 CDS，重复 2.5 次，总共 13 个 CDS。我们的基因组组装和手动管理发现在组装序列中插入了两个额外的 5S rRNA 基因拷贝，经 PCR 和 Sanger 测序证实为错误组装。该人工制品随后从最终组装中移除。在沙雷氏菌属的大多数完整基因组中也观察到了 5S rRNA 基因的额外拷贝。在我们的比较分析中存放在公共数据库中。这些元素也是自然发生的，很容易与真正的遗传变异相混淆。应该努力发现和纠正组装假象，以生成代表所研究生物体背后生物学真相的基因组序列。我们介绍了 N4-5 的基因组，并讨论了可能参与针对植物病原体的生物控制活动的基因，以及我们在初始组装中观察到的人工制品的可能机制。该报告提高了人们对已测序细菌基因组中 5S rRNA 基因的额外拷贝的认识，因为它们可能代表错误组装，因此应通过实验进行验证。