生物学杂志

生物学杂志 ›› 2024, Vol. 41 ›› Issue (5): 20-.doi: 10.3969/j.issn.2095-1736.2024.05.020

• 研究报告 • 上一篇    下一篇

产三峡肽素的草酸青霉SG-4的全基因组测序

张极峰， 白晓轩， 刘　超， 李　婧， 李　奥， 刘士平
  

  1. 三峡大学 生物与制药学院， 宜昌 443002
  • 出版日期:2024-10-18 发布日期:2024-10-14
  • 通讯作者: 刘士平，教授，博士生导师，主要从事微生物天然产物的教学与研究工作，E-mail:liuspain@ctgu.edu.cn
  • 作者简介:张极峰，硕士研究生，研究方向为非核糖体肽合成途径解析，E-mail:1696870630@qq.com
  • 基金资助:
    湖北省自然科学基金项目 (2023AFB188)

Whole genome sequencing of Penicillium oxalicum SG-4 producing Sanxiapeptin

#br# ZHANG Jifeng, BAI Xiaoxuan, LIU Chao, LI Jing, LI Ao, LIU Shiping #br# #br#   

  1. College of Life Science and Pharmacy, China Three Gorges University, Yichang 443002, China
  • Online:2024-10-18 Published:2024-10-14

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摘要： 为充分解析草酸青霉SG-4的遗传信息，利用二代Illumina测序和三代PacBio测序相结合的方法对SG-4的全基因组进行测序，经过基因组组装、基因预测和功能注释后，对全基因组进行共线性分析和次级代谢产物合成基因簇预测。结果表明，草酸青霉SG-4基因组全长为31.17 Mb，GC含量为50.5%，包括线粒体基因组在内，共由9条基因支架（scaffold）组成，含有8430个蛋白质编码基因、175个tRNA和50个rRNA基因。与swiss-prot、Pfam、NR、GO和KEGG等数据库相比，COG数据库注释的基因数最多，可达7483个。共线性分析结果表明，SG-4与数据库中报道的其他草酸青霉的同源性有一定差异，且存在多处异位重排现象。通过生物信息学分析发现，SG-4基因组中有28个次级代谢产物生物合成基因簇，其中,14个基因簇的功能未见报道，将NRPS相关基因簇与转录组数据进行对应的同时,分析与三峡肽素合成趋势的相关性，得到9条基因簇，经前期实验验证其中有一条可能是负责三峡肽素合成的候选基因簇。研究丰富了草酸青霉的基因组信息，为全面了解草酸青霉的基因组信息、揭示三峡肽素的生物合成途径奠定基础。

关键词: 草酸青霉, SG-4, 基因组, 基因注释, 三峡肽素

Abstract: To comprehensively analyze the genetic information ofPenicillium oxalicumSG-4, a combination of second-generation Illumina sequencing and third-generation PacBio sequencing was employed to sequence the complete genome of the SG-4 strain. Following genome assembly, gene prediction, and functional annotation, collinearity analysis was conducted on the whole genome and the gene clusters involved in secondary metabolite synthesis were predicted. The results showed that the genome size of SG-4 was 31.17 Mb, consisting of 9 scaffolds (including mitochondria), with GC content of 50.5%, and encompassing 8430 protein-coding genes along with 175 tRNA genes and 50 rRNA genes. Compared with the databases of swiss-prot, Pfam, NR, GO, and KEGG, the COG database annotated the largest number of genes to up to 7483. Through bioinformatics analysis, a total of 28 biosynthesis gene clusters of secondary metabolites were identified in the SG-4 genome, with 14 gene clusters having unknown functions. By correlating NRPS-related gene clusters with transcriptome data, the relationship between these gene clusters and the trend of Sanxiapeptin synthesis was analyzed, resulting in identification of 9 relevant gene clusters. Among them, one particular gene cluster might be a potential candidate responsible for Sanxiapeptin synthesis. This study enhanced our understanding ofP. oxalicum’s genomic information, laying a foundation for comprehensive characteristics as well as revealing the biosynthesis pathway of Sanxiapeptin.

Key words: Penicillium oxalicum, SG-4, genome, gene annotation, Sanxiapeptin

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