Spingobiumsp.PAMC28499与乌干达的冰川隔离。乌干达是一个独特的地区,炎热地区和冰川共存,有各种各样的生物存活下来,但是对他们的调查非常糟糕。Sphingobium菌株的遗传特征和完整的基因组信息有助于环境研究和更好的酶工业发展。
在这项研究中,Spingobiumsp的完整基因组序列。PAMC28499与该地区的Spinggobium物种菌株的比较分析。
使用PacBio序列单分子实时(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。并利用dbCAN2和KEGG数据库对碳水化合物活性酶(CAZymes)的降解途径进行了预测和蛋白质预测。
基因组序列的GC含量为64.5%,4432编码蛋白质编码基因,61个tRNA,和12个rRNA操纵子。它的基因组编码一组与果胶及其预测的降解蛋白相关的简单代谢途径,这是CAZymes与细胞外酯酶和果胶酸裂解酶的不寻常分布。CAZyme注释分析揭示了165个与碳水化合物活性相关的基因,特别是我们发现了GH1,GH2,GH3,GH38,GH35,GH51,GH51,GH53,GH106,GH146,CE12,PL1和PL11等已知的果胶降解基因。这些结果证实了这种鞘氨醇。菌株PAMC28499具有与RGI果胶降解途径相似的模式。
在这项研究中,分离并测序了Spingobiumsp。的完整基因组。PAMC28499。此外,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储存和产生能量。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。
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.
In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region.
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).
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.
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.