State Key Laboratory of Agricultural Microbiology, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
BMC Genet. 2020 Dec 18;21(Suppl 2):138. doi: 10.1186/s12863-020-00945-0.
Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to control insect pests of agricultural, veterinary, and human health importance. Irradiation of pupae in SIT can reduce the ecological fitness of the sterile insects. Our previous study has shown that a gut bacterial strain BD177 that could restore ecological fitness by promoting host food intake and metabolic activities.
Using long-read sequence technologies, we assembled the complete genome of K. michiganensis BD177 strain. The complete genome of K. michiganensis BD177 comprises one circular chromosome and four plasmids with a GC content of 55.03%. The pan-genome analysis was performed on 119 genomes (strain BD177 genome and 118 out of 128 published Klebsiella sp. genomes since ten were discarded). The pan-genome includes a total of 49305 gene clusters, a small number of 858 core genes, and a high number of accessory (10566) genes. Pan-genome and average nucleotide identity (ANI) analysis showed that BD177 is more similar to the type strain K. michiganensis DSM2544, while away from the type strain K. oxytoca ATCC13182. Comparative genome analysis with 21 K. oxytoca and 12 K. michiganensis strains, identified 213 unique genes, several of them related to amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotics biodegradation and metabolism in BD177 genome.
Phylogenomics analysis reclassified strain BD177 as a member of the species K. michiganensis. Comparative genome analysis suggested that K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis. The clear classification status of BD177 strain and identification of unique genetic characteristics may contribute to expanding our understanding of the symbiotic relationship of gut microbiota and B. dorsalis.
实蝇是一种破坏性的多食性和高度入侵性的热带和亚热带水果和蔬菜作物昆虫害虫。不育昆虫技术（SIT）已被用于控制农业、兽医和人类健康重要性的昆虫害虫数十年。在 SIT 中对蛹进行辐照可以降低不育昆虫的生态适应性。我们之前的研究表明，一种肠道细菌菌株 BD177 可以通过促进宿主的食物摄入和代谢活动来恢复生态适应性。
使用长读序列技术，我们组装了 K. michiganensis BD177 菌株的完整基因组。K. michiganensis BD177 菌株的完整基因组由一个圆形染色体和四个质粒组成，GC 含量为 55.03%。对 119 个基因组（菌株 BD177 基因组和 128 个已发布的 Klebsiella sp. 基因组中的 118 个，因为有 10566 个被丢弃）进行了泛基因组分析。泛基因组包括总共 49305 个基因簇、少量的 858 个核心基因和大量的辅助（10566 个）基因。泛基因组和平均核苷酸同一性（ANI）分析表明，BD177 与模式菌株 K. michiganensis DSM2544 更为相似，而与模式菌株 K. oxytoca ATCC13182 则不同。与 21 株 K. oxytoca 和 12 株 K. michiganensis 菌株的比较基因组分析确定了 213 个独特基因，其中一些与氨基酸代谢、辅酶和维生素代谢以及 BD177 基因组中的外来生物生物降解和代谢有关。
系统基因组学分析将菌株 BD177 重新归类为 K. michiganensis 种的成员。比较基因组分析表明，K. michiganensis BD177 具有为 B. dorsalis 提供三种必需氨基酸（苯丙氨酸、色氨酸和蛋氨酸）和两种维生素 B（叶酸和核黄素）的菌株特异性能力。BD177 菌株的明确分类地位和独特遗传特征的鉴定可能有助于扩大我们对肠道微生物群和 B. dorsalis 共生关系的理解。
