Valenzuela Ruiz Valeria, Santoyo Gustavo, Gómez Godínez Lorena Jacqueline, Cira Chávez Luis A, Parra Cota Fannie I, de Los Santos Villalobos Sergio
Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico.
Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Av. Francisco J. Múgica s/n, Edif. B-3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico.
Curr Res Microb Sci. 2023 May 23;4:100193. doi: 10.1016/j.crmicr.2023.100193. eCollection 2023.
TE3 is a strictly aerobic and Gram-stain-positive plant growth-promoting bacterium, motile and catalase-positive. In addition, strain TE3 was also recently described as a biological control agent. Here, we present the complete circularized genome of this type strain, as well as a whole genome analysis identifying genes of agricultural interest. Thus, a hybrid assembly method was performed using short-read sequencing through the Illumina MiSeq platform, and long-read sequencing through the MinION sequencing technology by Oxford Nanopore Technology (ONT). This assembly method showed a closed circular chromosome of 4,125,766 bp and 44.2% G + C content. The strain TE3 genome annotation, based on the RAST platform, presented 4,282 Coding DNA sequences (CDS) distributed in 335 subsystems, from which 4 CDS are related to the promotion of plant growth and 28 CDS to biological control. Also, Prokka (Rapid Prokaryotic Genome Annotation) predicted a total of 119 RNAs composed of 87 tRNAs, 31 rRNA, and 1 tmRNA; and the PGAP (Prokaryotic Genome Annotation Pipeline) predicted a total of 4,212 genes (3,991 CDS). Additionally, seven putative biosynthetic gene clusters were identified by antiSMASH, such as Fengycin, Bacilysin, Subtilosin A, Bacillibactin, Bacillaene, Surfactin, and Rizocticin A, which are related to antimicrobial and antifungal properties, whose gene presence was further supported by the Prokaryotic Genome Annotation Pipeline (PGAP) annotation. Thus, the complete genome of TE3 showed promising bioactivities for the use of this type strain to bioformulate bacterial inoculants for sustainable agriculture.
TE3是一种严格需氧且革兰氏染色阳性的植物促生细菌，具运动性且过氧化氢酶呈阳性。此外，菌株TE3最近还被描述为一种生物防治剂。在此，我们展示了该模式菌株的完整环状基因组，以及一项全基因组分析，鉴定出具有农业应用价值的基因。因此，采用了一种混合组装方法，通过Illumina MiSeq平台进行短读长测序，并通过牛津纳米孔技术（ONT）的MinION测序技术进行长读长测序。这种组装方法显示出一条长度为4,125,766 bp、G + C含量为44.2%的闭合环状染色体。基于RAST平台的菌株TE3基因组注释显示，有4,282个编码DNA序列（CDS）分布在335个子系统中，其中4个CDS与植物生长促进有关，28个CDS与生物防治有关。此外，Prokka（快速原核生物基因组注释）预测共有119个RNA，包括87个tRNA、31个rRNA和1个tmRNA；而PGAP（原核生物基因组注释管道）预测共有4,212个基因（3,991个CDS）。另外，antiSMASH鉴定出7个假定的生物合成基因簇，如丰原素、芽孢溶菌素、枯草菌素A、杆菌铁载体、杆菌烯、表面活性素和根际菌素A，它们与抗菌和抗真菌特性有关，其基因的存在得到了原核生物基因组注释管道（PGAP）注释的进一步支持。因此，TE3的完整基因组显示出该模式菌株在用于可持续农业的细菌接种剂生物配方方面具有良好的生物活性。
