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Complete genome sequence of Rhodoferax sp. PAMC 29310 from a marine sediment of the East Siberian Sea
Marine Genomics ( IF 1.3 ) Pub Date : 2021-09-04 , DOI: 10.1016/j.margen.2021.100891
Yung Mi Lee 1 , Yerin Park 2 , Heesoo Kim 1 , Seung Chul Shin 1
Affiliation  

Rhodoferax sp. PAMC 29310 was isolated from a surface marine sediment of the East Siberian Sea, Arctic. Whole-genome sequencing of the strain Rhodoferax sp. PAMC 29310 was achieved using PacBio RS II and Illumina platform. The resulting complete genome comprised of 4,593,249 base pairs (G + C content of 58.0%) with a single chromosome, 4546 protein-coding genes, 57 tRNAs and 6 rRNA operons. A complete set of genes encoding the enzymes of glycolysis and citric acid cycle were identified. No genes encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and nitrogenase reductase (nif) were present indicating that strain PAMC 29310 is not capable of fixing of carbon and nitrogen. PAMC 29310 genome contains genes for dissimilatory and assimilatory nitrate reduction. Gene encoding choline dehydrogenase enzyme which functions at the first step in the synthesis of betaine, one of the most effective osmoprotectants, was detected. In particular, among the genomes of the genus Rhodoferax strains, gene encoding nitrite reductase (nirK), which reduces nitrite to nitric oxide and tetA gene encoding tetracycline resistance protein involved in the resistance to tetracycline were identified only in the genome of Rhodoferax sp. PAMC 29310. As the first genome from the strain which was isolated from marine sediment in the genus Rhodoferax, investigation of physiological characteristics based on the complete genome sequences will help understand the adaptation of Rhodoferax sp. PAMC 29310 in the marine sediment.



中文翻译:

Rhodoferax sp的完整基因组序列。PAMC 29310 来自东西伯利亚海的海洋沉积物

红花属 PAMC 29310 是从北极东西伯利亚海的表层海洋沉积物中分离出来的。菌株Rhodoferax sp的全基因组测序。PAMC 29310 是使用 PacBio RS II 和 Illumina 平台实现的。得到的完整基因组由 4,593,249 个碱基对(G + C 含量为 58.0%)组成,具有单个染色体、4546 个蛋白质编码基因、57 个 tRNA 和 6 个 rRNA 操纵子。鉴定出一整套编码糖酵解和柠檬酸循环酶的基因。没有编码核酮糖 1,5-二磷酸羧化酶/加氧酶 (RuBisCO) 和固氮酶还原酶 ( nif) 的存在表明菌株 PAMC 29310 不能固定碳和氮。PAMC 29310 基因组包含异化和同化硝酸盐还原的基因。检测到编码胆碱脱氢酶的基因,该酶在甜菜碱合成的第一步起作用,甜菜碱是最有效的渗透保护剂之一。特别是,在Rhodoferax属菌株的基因组中,仅在Rhodoferax的基因组中发现了编码亚硝酸盐还原酶 ( nir K) 的基因,该基因将亚硝酸盐还原为一氧化氮,以及编码四环素抗性蛋白的tetA基因参与了对四环素的抗性。sp。PAMC 29310. 作为从海洋沉积物中分离出的Rhodoferax属菌株的第一个基因组,基于完整基因组序列的生理特征调查将有助于了解Rhodoferax sp的适应性。海洋沉积物中的 PAMC 29310。

更新日期:2021-09-04
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