Genome analysis of Pseudomonas spp. CPA-7, a strain with potential as a biocontrol agent

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-08-26 DOI:10.1016/j.genrep.2025.102326

Cyrelys Collazo , Jose Francisco Sanchez-Herrero , Rui Alves , Julio Rozas , Isabel Alegre , Abdelrhaman Eleiwa , Inmaculada Viñas

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Abstract

We report the whole genome sequence of CPA-7, a strain isolated from apple surface and classified as Pseudomonas graminis, that has shown antagonistic activity against pathogenic bacteria in several food matrices. Its genome comprises 5,786,948 bp, with 60.5 % average of C + G content. From the 5122 predicted protein coding sequences (CDSs), 4703 (91.8 %) were functionally annotated. Comparative genomic analyses using 366 fully sequenced Pseudomonas strains placed CPA-7 within the P. lutea group, more related to P. graminis UASWS1507. However, ANI values in respect to the other fully sequenced P. graminis (91–92 %), including the type strain DSM11363, were below the intraspecific bacterial threshold (95 %). Whole genomic digital DNA-DNA hybridization in the Type Strain Genome Server also gave a below threshold score for P. graminis (47.7 %), suggesting the need for revision of this taxon. BLAST analyses of 16S rRNA showed >99 % identity with other Pseudomonas spp. while the rpoD amplified sequence revealed a 100 % similarity with Pseudomonas sp. Irchel 1A17. Single orthologs analysis unraveled 341 CDSs unique to CPA-7 compared to the rest of P. graminis strains including genes involved in transport, adherence, and adaptability. Genome mining uncovered genes potentially involved in biological control, and plant growth promoting activities which corresponded to in vitro activities such as the production of siderophores, 1-aminocyclopropane-1-carboxylate deaminase, and Indole-3-acetic acid as well as Phosphorous solubilization. Furthermore, multiple genes associated with chemotaxis, colonization, and metabolic plasticity, unravel the genetic basis for the potentialities of CPA-7 as a biocontrol agent, opening several lines for further investigation.

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具有生物防治潜力的假单胞菌CPA-7的基因组分析

我们报道了从苹果表面分离的一株被归类为谷草假单胞菌的CPA-7的全基因组序列，该菌株对几种食物基质中的致病菌具有拮抗活性。其基因组全长5,786,948 bp， C + G含量平均为60.5%。在5122个预测的蛋白编码序列（CDSs）中，4703个（91.8%）被功能注释。利用366个全测序假单胞菌菌株进行比较基因组分析，发现CPA-7属于P. lutea组，与P. graminis UASWS1507更相关。然而，对于其他完全测序的禾草假单胞菌（91 - 92%），包括型菌株DSM11363， ANI值低于种内细菌阈值（95%）。全基因组数字DNA-DNA杂交在型菌株基因组服务器上也给出了低于阈值的评分（47.7%），表明该分类单元需要修订。BLAST分析显示，16S rRNA与其他假单胞菌属的同源性为99%，而rpoD扩增序列与假单胞菌属Irchel 1A17的同源性为100%。单一同源物分析揭示了CPA-7与其他禾草假单胞菌菌株相比所特有的341个CDSs，包括参与运输、粘附和适应性的基因。基因组挖掘发现了可能参与生物控制和植物生长促进活性的基因，这些活性与铁载体的产生、1-氨基环丙烷-1-羧酸脱氨酶、吲哚-3-乙酸以及磷的溶解等体外活性相对应。此外，与趋化性、定植和代谢可塑性相关的多个基因揭示了CPA-7作为生物防治剂潜力的遗传基础，为进一步研究开辟了几个领域。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.