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0916-4-2的全基因组序列及其比较基因组分析

Complete Genome Sequence of 0916-4-2 and Its Comparative Genomic Analysis.

作者信息

Panthee Suresh, Paudel Atmika, Blom Jochen, Hamamoto Hiroshi, Sekimizu Kazuhisa

机构信息

Institute of Medical Mycology, Teikyo University, Hachioji, Japan.

Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.

出版信息

Front Microbiol. 2019 Jul 24;10:1619. doi: 10.3389/fmicb.2019.01619. eCollection 2019.

Abstract

genus from Leuconostocaceae family forms a group of Gram-positive lactic acid bacteria (LAB) that mostly reside in fermented foods and some have been isolated from the environment and vertebrates including humans. Currently there are 23 recognized species, 16 complete and 37 draft genome assemblies for this genus. has been found in various sources and is characterized by their probiotic and bacteriocinogenic properties. Despite its widespread importance, little attention has been paid to genomic characterization of this species with the availability of draft assembly of two species in the public database so far. In this manuscript, we identified 0916-4-2 from fermented kimchi and completed its genome sequence. Comparative genomic analysis identified 88 core genes that had interspecies mean amino acid identity of more than 65%. Whole genome phylogenetic analysis showed that three strains clustered together and the strain 0916-4-2 was close to strain WiKim14. analysis for the secondary metabolites biosynthetic gene cluster showed that are far less producers of secondary metabolites compared to other members of Leuconostocaceae. The availability of the complete genome of 0916-4-2 will facilitate further comparative genomic analysis of species, including studies of its biotechnological potential and improving the nutritional value of various food products.

摘要

明串珠菌科的该属形成了一组革兰氏阳性乳酸菌(LAB),它们大多存在于发酵食品中,一些已从环境以及包括人类在内的脊椎动物中分离出来。目前该属有23个已确认的物种、16个完整基因组和37个草图基因组组装。已在各种来源中发现其具有益生菌和产细菌素的特性。尽管其具有广泛的重要性,但到目前为止,由于公共数据库中仅有两个物种的草图组装,对该物种的基因组特征研究较少。在本手稿中,我们从发酵泡菜中鉴定出0916 - 4 - 2并完成了其基因组序列。比较基因组分析确定了88个核心基因,这些基因的种间平均氨基酸同一性超过65%。全基因组系统发育分析表明,三个菌株聚集在一起,菌株0916 - 4 - 2与菌株WiKim14关系密切。对次生代谢物生物合成基因簇的分析表明,与明串珠菌科的其他成员相比,该属产生次生代谢物的能力要低得多。0916 - 4 - 2完整基因组的可得性将有助于对该属物种进行进一步的比较基因组分析,包括对其生物技术潜力的研究以及提高各种食品的营养价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/357c/6667553/4c046719f001/fmicb-10-01619-g001.jpg

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