Malbranchea zuffiana 前型菌株的基因组测序和功能分析

IF 4.2 2区 生物学 Q2 MICROBIOLOGY Journal of Fungi Pub Date : 2024-08-24 DOI:10.3390/jof10090600
Alan Omar Granados-Casas, Ana Fernández-Bravo, Alberto Miguel Stchigel, José Francisco Cano-Lira
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引用次数: 0

摘要

Malbranchea 是子囊菌目(子囊菌门)中的一个属,主要包括有袋孢子的世界性物种。尽管 Malbranchea 能产生多种次级代谢产物,但目前数据库中还没有 Malbranchea 属的基因组数据。因此,在本研究中,我们获得了 Malbranchea zuffiana 前型菌株(CBS 219.58)的基因组序列,并对其进行了组装和注释。在基因组测序中,我们使用了 Illumina 和 PacBio 平台,然后使用 MaSuRCA 进行了混合组装。利用 QUAST 和 BUSCO 工具对组装结果进行了质量评估。使用 BRAKER2 进行了注释,并使用 InterProScan 完成了功能注释。所得到的基因组质量很高,大小为 26.46 Mbp,分布在 38 个等位基因上,BUSCO 完成率为 95.7%,表明基因组的连续性和组装完整性非常好。共预测了 8248 个编码蛋白质的基因,其中 73.9% 的基因被赋予了功能注释。此外,82 个基因与病原体宿主相互作用(PHI)数据库中的条目显示出同源性,494 个基因与碳水化合物活性酶(CAZymes)数据库中的条目显示出相似性。此外,还发现了 30 个生物合成基因簇 (BGC),这表明生物合成各种次级代谢物的潜力巨大。通过与近缘物种的功能比较分析发现,在所有研究的鬼针草属物种中,与参与角蛋白降解的酶相关的结构域相当丰富,而与参与植物细胞壁降解的酶相关的结构域数量有限。这种基于基因组的阐释不仅提高了我们对 M. zuffiana 生物特征的理解,而且还为后续有关 Malbranchea 物种和 Onygenales 目植物的研究提供了宝贵的见解。
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Genomic Sequencing and Functional Analysis of the Ex-Type Strain of Malbranchea zuffiana
Malbranchea is a genus within the order Onygenales (phylum Ascomycota) that includes predominantly saprobic cosmopolitan species. Despite its ability to produce diverse secondary metabolites, no genomic data for Malbranchea spp. are currently available in databases. Therefore, in this study, we obtained, assembled, and annotated the genomic sequence of the ex-type strain of Malbranchea zuffiana (CBS 219.58). For the genomic sequencing, we employed both the Illumina and PacBio platforms, followed by hybrid assembly using MaSuRCA. Quality assessment of the assembly was performed using QUAST and BUSCO tools. Annotation was conducted using BRAKER2, and functional annotation was completed with InterProScan. The resulting genome was of high quality, with a size of 26.46 Mbp distributed across 38 contigs and a BUSCO completion rate of 95.7%, indicating excellent contiguity and assembly completeness. A total of 8248 protein-encoding genes were predicted, with functional annotations assigned to 73.9% of them. Moreover, 82 genes displayed homology with entries in the Pathogen Host Interactions (PHI) database, while 494 genes exhibited similarity to entries in the Carbohydrate-Active Enzymes (CAZymes) database. Furthermore, 30 biosynthetic gene clusters (BGCs) were identified, suggesting significant potential for the biosynthesis of diverse secondary metabolites. Comparative functional analysis with closely related species unveiled a considerable abundance of domains linked to enzymes involved in keratin degradation, alongside a restricted number of domains associated with enzymes engaged in plant cell wall degradation in all studied species of the Onygenales. This genome-based elucidation not only enhances our comprehension of the biological characteristics of M. zuffiana but also furnishes valuable insights for subsequent investigations concerning Malbranchea species and the order Onygenales.
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来源期刊
Journal of Fungi
Journal of Fungi Medicine-Microbiology (medical)
CiteScore
6.70
自引率
14.90%
发文量
1151
审稿时长
11 weeks
期刊介绍: Journal of Fungi (ISSN 2309-608X) is an international, peer-reviewed scientific open access journal that provides an advanced forum for studies related to pathogenic fungi, fungal biology, and all other aspects of fungal research. The journal publishes reviews, regular research papers, and communications in quarterly issues. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. Therefore, there is no restriction on paper length. Full experimental details must be provided so that the results can be reproduced.
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