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泛基因组评估:深入研究海洋附生植物菌株19_A及来自多种环境的其他亲缘关系极近的菌株的基因组。

A pan-genomic assessment: Delving into the genome of the marine epiphyte strain 19_A and other very close strains from multiple environments.

作者信息

Comba-González Natalia Beatriz, Chaves-Moreno Diego, Santamaría-Vanegas Johanna, Montoya-Castaño Dolly

机构信息

Biological and Environmental Sciences Area, Jorge Tadeo Lozano University, Colombia.

Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.

出版信息

Heliyon. 2024 Mar 20;10(7):e27820. doi: 10.1016/j.heliyon.2024.e27820. eCollection 2024 Apr 15.

Abstract

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of sp. and a codon bias assessment, including the genome of the strain 19_A and 29 complete genome sequences of closely related strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.

摘要

海洋大型藻类是附生细菌的栖息地,并为有益的生物相互作用蓬勃发展提供了多种条件。尽管[具体属名]是最丰富的附生属之一,但关于与海洋大型藻类相关的[该属名]物种的基因组信息仍然匮乏。在本研究中,我们进一步研究了我们之前发表的附生菌株19_A的基因组,以寻找可转化为该微生物产生的潜在代谢物的特征,以及在其与大型藻类宿主相互作用中发挥作用的基因。为实现这一目标,我们对[该属名]菌进行了泛基因组分析和密码子偏好性评估,包括菌株19_A的基因组以及从土壤、海洋环境、植物、极端环境、空气和食物中分离出的29个密切相关的[该属名]菌株的完整基因组序列。这种基因组分析表明,19_A拥有编码参与水平基因转移、DNA修复、转录调控和细菌素生物合成的蛋白质的独特基因。在这种比较分析中,密码子偏好性与所研究菌株的栖息地无关。在19_A基因组中鉴定出了一些可能与其附生生活方式相关的辅助基因,以及用于孢子形成杀伤因子和细菌素生物合成的基因簇,显示出它们作为抗菌肽来源的潜力。我们的结果提供了对19_A基因组的全面认识,以了解其对海洋环境的适应性及其作为生物活性化合物生产者的潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bebc/10981035/7665f0cd9fc0/gr1.jpg

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