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海洋放线菌次生代谢生物合成基因簇分布的比较基因组学研究

Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine .

机构信息

Lab of Marine Functional Molecules, Zhejiang Sci-Tech University, Hangzhou 310018, China.

College of Life Sciences and Medicine, Zhejiang Sci-Tech Univeristy, Hangzhou 310018, China.

出版信息

Mar Drugs. 2019 Aug 26;17(9):498. doi: 10.3390/md17090498.

DOI:10.3390/md17090498
PMID:31454987
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6780079/
Abstract

Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine is a valuable resource of bacterial secondary metabolites. In this study, 87 marine genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine and developing their secondary metabolites in the future.

摘要

细菌次生代谢产物在多个行业具有巨大的应用潜力。细菌次生代谢产物的生物合成通常由一组基因编码，这些基因组织在次生代谢生物合成基因簇（SMBGCs）中。基因组测序技术的发展促进了细菌 SMBGC 的挖掘。海洋是细菌次生代谢产物的宝贵资源。本研究获得了 87 个海洋 基因组，并进行了比较基因组分析，结果表明由于泛基因组拥有 123302 个直系同源簇，它们具有很高的遗传多样性。系统发育基因组分析表明，大多数海洋 被分为三个分支，分别命名为 I 类、II 类和 III 类，分别包含 23、38 和 22 株。基因组注释表明，海洋 基因组中的 SMBGC 数量从 16 到 84 不等。统计分析指出，基因型和生态型都与 SMBGC 的分布模式有关。I 类和海洋沉积物来源的 携带更多特定的 SMBGC，其中包括几个常见的 SMBGC；而 II 类和海洋无脊椎动物来源的 携带更多的 SMBGC，作为次生代谢产物挖掘的更丰富资源。本研究有助于拓宽我们对海洋 中 SMBGC 分布模式的认识，并为未来开发其次生代谢产物提供帮助。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/d885e837e8af/marinedrugs-17-00498-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/934b8a730c63/marinedrugs-17-00498-g001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/503e2c1b8b28/marinedrugs-17-00498-g003.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/7af2c6ec2205/marinedrugs-17-00498-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/d885e837e8af/marinedrugs-17-00498-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/934b8a730c63/marinedrugs-17-00498-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/c3d98d89f962/marinedrugs-17-00498-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/503e2c1b8b28/marinedrugs-17-00498-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/5a1106333b3a/marinedrugs-17-00498-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/7af2c6ec2205/marinedrugs-17-00498-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d97/6780079/d885e837e8af/marinedrugs-17-00498-g006.jpg

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