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DSM 21565的基因组序列草图,DSM 21565是从哥伦比亚盐泉中分离出的一种厌氧、轻度嗜盐细菌。

Draft genome sequence of DSM 21565 an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.

作者信息

Díaz-Cárdenas Carolina, López Gina, Alzate-Ocampo José David, González Laura N, Shapiro Nicole, Woyke Tanja, Kyrpides Nikos C, Restrepo Silvia, Baena Sandra

机构信息

Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia.

Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, DC Colombia.

出版信息

Stand Genomic Sci. 2017 Dec 20;12:86. doi: 10.1186/s40793-017-0303-x. eCollection 2017.

Abstract

A bacterium belonging to the phylum , genus was isolated in 2007 from a saline spring in Colombia. USBA 82 ( is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species USBA 82. The genome consisted of 2.68 Mbp with a 53.7% G + C A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82 genome six conserved signature indels (CSIs), specific for and . The genome of contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of , related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.

摘要

2007年,从哥伦比亚的一个盐泉中分离出一种属于某门、某属的细菌。USBA 82是一种嗜温、严格厌氧、轻度嗜盐的革兰氏阴性细菌,具有双层细胞膜。该菌株可发酵肽、氨基酸和一些有机酸。在此,我们展示了模式菌株USBA 82的全基因组测序和注释描述。基因组由2.68 Mbp组成,G + C含量为53.7%。共预测出2609个基因,其中2543个为蛋白质编码基因,66个为RNA基因。我们在USBA 82基因组中检测到六个保守特征插入缺失(CSI),它们是某属和某属特有的。正如预期的那样,某属的基因组包含与氨基酸转运、氨基酸代谢和硫代硫酸盐还原相关的基因。这些基因代表了某属与其表型特征相关的主要基因组,有趣的是,基因组中11.8%的基因属于氨基酸发酵COG类别。此外,我们在基因组中鉴定出一些氨化基因,如硝酸还原酶基因。脯氨酸操纵子基因的存在可能与脯氨酸的从头合成有关,以保护细胞应对高渗透压。我们的生物信息学工作流程包括antiSMASH和BAGEL3,这使我们能够在基因组中鉴定出细菌素基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/27a6/5738826/a228aecdfa34/40793_2017_303_Fig1_HTML.jpg

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