Plant Pathology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
Braz J Microbiol. 2021 Mar;52(1):245-250. doi: 10.1007/s42770-020-00382-2. Epub 2020 Sep 23.
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.
粘质沙雷氏菌是一种革兰氏阴性细菌，存在于多个环境小生境中，包括植物根际和医院患者。在这里，我们介绍了粘质沙雷氏菌菌株 N4-5（=NRRL B-65519）的基因组，其大小为 5074473bp（664 倍覆盖率），包含 4840 个蛋白质编码基因、21 个 RNA 基因，平均 G+C 含量为 59.7%。N4-5 含有一个 11089bp 的质粒，G+C 含量为 43.5%，编码 6 个独特的 CDS，重复 2.5 倍，总计 13 个 CDS。我们的基因组组装和手动注释发现，在组装序列中插入了两个额外的 5S rRNA 基因副本，通过 PCR 和 Sanger 测序证实这是一个错误组装。随后，该错误组装从最终组装中被移除。在我们的比较分析中，从公共数据库中存储的大多数粘质沙雷氏菌属的完整基因组中也观察到了 5S rRNA 基因的额外副本。这些元素也自然存在，很容易与真正的遗传变异混淆。为了生成代表所研究生物的生物学真相的基因组序列，应该努力发现和纠正组装错误。我们展示了 N4-5 的基因组，并讨论了可能参与对植物病原体的生物防治活性的基因，以及我们在初始组装中观察到的可能导致该错误的机制。本报告提高了人们对测序细菌基因组中 5S rRNA 基因额外副本的认识，因为它们可能代表错误组装，因此应通过实验进行验证。
