44 种早期分化真菌中的王国间水平基因转移提高了它们的代谢、适应和免疫能力。

IF 4.3 3区 材料科学 Q1 ENGINEERING, ELECTRICAL & ELECTRONIC
ACS Applied Electronic Materials Pub Date : 2024-03-05 eCollection Date: 2024-08-01 DOI:10.1093/evlett/qrae009
Michał Aleksander Ciach, Julia Pawłowska, Paweł Górecki, Anna Muszewska
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引用次数: 0

摘要

关于真菌中横向获得基因的个案研究不胜枚举。研究表明,这些基因扩大了宿主的新陈代谢能力,有助于宿主适应寄生或共生环境。一些研究对 Dikarya 中的水平基因转移(HGT)进行了广泛的描述。然而,在早期分化真菌(EDF)中,类似的特征描述仍然缺失。为了填补这一空白,我们设计了一个计算管道,以获得可靠的 HGT 事件统计样本,同时降低错误发现率。我们分析了 44 个 EDF 蛋白体组,在从栉水母纲到粘菌纲的真菌中发现了 829 个异源物。我们发现了 EDF HGT 的几种模式和统计特性。我们的研究表明,HGT 是由基因交换和复制的爆发所驱动的,从而导致真菌品系之间的异源物在数量和分子特性上的高度差异。水生真菌比陆生真菌更容易获得外来遗传物质。内共生细菌可能是有用的异源物的来源,例如转移到毛霉菌群中的 NOD 样受体。近缘真菌也有类似的异源基因内含率。转移后基因融合和蛋白质结构域缺失很常见,可能会影响编码蛋白质的功能。我们认为,目前还没有一种通用的方法来鉴定 HGT,王国之间和王国内部的转移需要量身定制的鉴定方法。我们的研究结果有助于更好地理解 HGT 如何以及在多大程度上塑造了真菌的代谢、适应和免疫能力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.

Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.

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来源期刊
CiteScore
7.20
自引率
4.30%
发文量
567
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