Background

Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry.

Objective

In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region.

Methods

Genome sequencing was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes).

Results

The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway.

Conclusion

In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.

中文翻译：

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Sphingobium sp。的完整基因组序列。PAMC 28499菌株显示了使用比较基因组学方法降解果胶的潜力。

背景

螺孢菌 PAMC 28499与乌干达冰川隔离。乌干达是炎热地区和冰川共存的独特地区，有各种生物在其中生存，但是对它们的调查非常糟糕。鞘氨醇单胞菌菌株的遗传特性和完整的基因组信息有助于环境研究和向酶工业的发展。

目的

在这项研究中，Spingobium sp。的完整基因组序列。PAMC 28499以及从该地区不同地区分离到的Spingobium种菌株的比较分析。

方法

使用PacBio sequel单分子实时（SMRT）测序技术进行基因组测序。对预测的基因序列进行功能注释，并使用程序NCBI非冗余数据库进行基因预测。并使用dbCAN2和KEGG数据库预测了碳水化合物活性酶（CAZymes）的降解途径和蛋白质预测。

结果

基因组序列具有64.5％的GC含量，4432个编码蛋白编码基因，61个tRNA和12个rRNA操纵子。它的基因组编码与果胶及其预测的降解蛋白有关的简单代谢途径集，以及带有细胞外酯酶和果胶酸裂合酶的CAZymes的异常分布。CAZyme注释分析揭示了165个与碳水化合物活性相关的基因，尤其是我们发现了GH1，GH2，GH3，GH38，GH35，GH51，GH51，GH53，GH106，GH146，CE12，PL1和PL11等已知的果胶降解基因，这些基因来自于phingobium yanoikuiae。这些结果证实了该鞘氨醇单胞菌。菌株PAMC 28499具有与RG I果胶降解途径相似的模式。

结论

在这项研究中，分离并测序了Spingobium sp。的完整基因组。PAMC28499。而且，该菌株具有比较基因组分析。通过完整的基因组，我们可以预测该菌株如何在极端环境中存储和产生能量。它还可以通过发现降解果胶的新基因来提供生物工程数据。