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利用木质纤维素类生物质产微生物絮凝剂Pseudomonas boreopolis GO2的全基因组测序及比较基因组学分析
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国家自然科学基金(21801143);宁波市公益计划(2019C10077)


Genome sequencing and comparative genome analysis of Pseudomonas boreopolis GO2, a strain producing bioflocculant with lignocellulosic biomass
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    摘要:

    【目的】Pseudomonas boreopolis GO2可以利用木质纤维素类生物质为唯一碳源发酵产微生物絮凝剂。解析菌株GO2的全基因组特征可为利用木质纤维素类生物质定向合成多糖型微生物絮凝剂提供分子基础。【方法】利用Illumina NovaSeq测序平台对菌株GO2进行测序,用SMRT等软件进行基因组组装、系统发育分析、基因预测和功能注释,并与4株近缘模式株进行了比较基因组分析。【结果】菌株GO2基因组大小为4 498 896 bp,GC含量为69.5%,共编码3 906个基因。菌株GO2与Pseudomonas boreopolis JCM 13306的16S rRNA基因相似性、平均核苷酸一致性(average nucleotide identity, ANI)、DNA-DNA杂交(DNA-DNA hybridization, DDH)值最高,分别为99.93%、98.36%和88.00%,将菌株GO2命名为Pseudomonas boreopolis GO2。比较基因组分析发现,GO2与4个近缘模式菌株共有2 348个直系同源核心基因,主要参与碳水化合物代谢、氨基酸代谢以及能量代谢等过程,而GO2菌株特有的307个基因主要与转录、复制、修复、细胞壁/膜/包膜的生物发生相关。菌株GO2基因组中含有226个碳水化合物活性酶(carbohydrate-active enzymes, CAZymes)基因,占总基因数的5.79%,包括82个与植物细胞壁降解相关的糖苷水解酶(glycoside hydrolases, GHs)家族基因和由糖基转移酶(glycosyltransferases, GTs)家族基因形成的3个多糖合成基因簇。【结论】根据菌株GO2基因组序列的比对分析,将其命名为Pseudomonas boreopolis GO2,其基因组中包含丰富的植物细胞壁降解酶基因和3个多糖合成基因簇,这些基因可能在菌株GO2直接利用木质纤维素类生物质合成微生物絮凝剂过程中发挥着重要作用。

    Abstract:

    [Objective] Pseudomonas boreopolis GO2 synthesizes bioflocculant with lignocellulosic biomass. In this study, the whole genome sequencing and comparative genome analysis of GO2 were performed to explore its genome characteristics and analyze genes related to lignocellulose degradation and polysaccharide bioflocculant synthesis. [Methods] Illumina NovaSeq was used for genome sequencing, and SMRT and other software for genome assembly, phylogenetic analysis, and gene prediction and annotation. Moreover, the genome was respectively compared with that of four similar model strains. [Results] The genome of GO2 was 4 498 896 bp, with guanine-cytosine (GC) content of 69.5% and 3 906 coding genes. It showed the highest 16S rRNA gene similarity (99.93%), DNA-DNA hybridization (DDH) (88.00%), and average nucleotide identity (ANI) (98.36%) to P. boreopolis JCM 13306. Therefore, this strain was named as P. boreopolis GO2. GO2 shared 2 348 core orthologous genes with the four model strains, and these genes were mainly involved in the pathways of carbohydrate metabolism, amino acid metabolism, and energy metabolism. The 307 specific genes of GO2 were mainly involved in the pathways of transcription, replication, repair, and cell wall/membrane biogenesis. GO2 contained 226 carbohydrate-active enzymes (CAZymes) genes, accounting for 5.79% of the total number of genes. Among the CAZymes genes, 82 belonged to the glycoside hydrolases (GHs) family which was related to plant cell wall degradation and 3 clusters of polysaccharide synthesis genes were formed by glycosyltransferases (GTs) family genes. [Conclusion] Based on the comparative analysis of genome sequences, GO2 is named Pseudomonas boreopolis GO2, and its genome contains rich plant cell wall degrading enzyme genes and three polysaccharide synthesis gene clusters, which may play an important role in the synthesis of bioflocculants by with lignocellulosic biomass in GO2.

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冯嘉茵,何继堃,孙嘉怡,符学志,袁佳骜,郭海朋. 利用木质纤维素类生物质产微生物絮凝剂Pseudomonas boreopolis GO2的全基因组测序及比较基因组学分析. 微生物学报, 2023, 63(2): 786-804

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  • 收稿日期:2022-06-28
  • 最后修改日期:
  • 录用日期:2022-09-07
  • 在线发布日期: 2023-02-21
  • 出版日期: 2023-02-04