Complete genome sequence of Kordiimonas pumila N18T sheds light on biogeochemical roles of the genus Kordiimonas

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Accounts of Chemical Research Pub Date : 2022-04-01 DOI:10.1016/j.margen.2022.100930

Nan Geng , Di Yang , Jia Hua , Long-Jia Huang , Han Dong , Cong Sun , Lin Xu

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引用次数: 3

Abstract

Kordiimonas pumila N18^T (=KCTC 62164^T = MCCC 1K03436^T) was isolated from coastal sediments collected in Zhoushan, P. R. China. Ensuing genome sequencing revealed that it consists of a single chromosome with a size of 4,041,658 bp and a DNA G+C content of 47.4%. The genomic annotations further identified 3724 open reading frames (ORFs), 4 rRNA genes, and 43 tRNA genes in the Kordiimonas pumila N18^T genome. The percentages of ORFs assigned to the CAZy, COG, GO, and KEGG databases were 1.0, 84.8, 19.9, and 59.3%, respectively. Comparative genomic analysis with four other Kordiimonas genomes indicated that the pan- and core-genomes of the genus Kordiimonas consists of 8985 and 1470 orthologous clusters, respectively. Functional annotations of the genus Kordiimonas core genome further revealed that they utilize monosaccharides, peptides, and esters as energy substrates because of the absence of several glycoside hydrolases, glycosyl transferases, aminopeptidases, carbohydrate esterase coding genes, and polysaccharide lyases coding genes in their genomes. Moreover, the genus Kordiimonas possesses survival advantages in ammonium-, phosphorus-, and iron- deficient environments, which are vital for inhabiting marine environments. Overall, this study reports the complete genome of the order Kordiimonadales and broadens the understanding of its ecological roles.

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Kordiimonas pumila N18T的全基因组序列揭示了Kordiimonas属的生物地球化学作用。

从舟山海岸沉积物中分离到一株短孢单胞菌N18T (=KCTC 62164T = MCCC 1K03436T)。随后的基因组测序显示，它由一条染色体组成，长度为4,041,658 bp, DNA G+C含量为47.4%。基因组注释进一步鉴定了Kordiimonas pumila N18T基因组中的3724个开放阅读框(orf)、4个rRNA基因和43个tRNA基因。分配给CAZy、COG、GO和KEGG数据库的orf百分比分别为1.0、84.8%、19.9%和59.3%。与其他4个Kordiimonas基因组的比较分析表明，Kordiimonas属的泛基因组和核心基因组分别由8985个和1470个同源簇组成。Kordiimonas属核心基因组的功能注释进一步表明，它们利用单糖、肽和酯作为能量底物，因为它们的基因组中缺乏几种糖苷水解酶、糖基转移酶、氨基肽酶、碳水化合物酯酶编码基因和多糖裂解酶编码基因。此外，Kordiimonas属在缺乏铵、磷和铁的环境中具有生存优势，这对海洋环境的生存至关重要。总的来说，本研究报道了Kordiimonadales的完整基因组，拓宽了对其生态作用的认识。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.

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