Phylogenetic Relationships of Three Ramaria Species Based on Mitochondrial Genome Analysis

IF 2.3 2区生物学 Q2 ECOLOGY

Ecology and Evolution Pub Date : 2025-02-12 DOI:10.1002/ece3.70901

Xianyi Wang, Zhongyao Guo, Jiawei Tao, Gongyou Zhang, Guoyu Wang, Yaping Wang, Yaohang Long, Hongmei Liu

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Abstract

Ramaria has been a remarkable genus throughout the history of macrofungi. However, there is a lack of information on this genus of macrofungi. This study determined the order of nucleotides in the mitochondrial genomes (mitogenomes) of three Ramaria species, followed by a detailed investigation of the obtained genetic information. Circular mitogenomes of Ramaria brunnecliacina, R. ichnusensis, and R. flavescens had sizes of 78,960, 61,851, and 81,282 bp, respectively. The genomes exhibited variations in genetic content, gene length, tRNA, and codon usage. Ramaria mitogenomes demonstrated variable evolutionary rates across several protein-coding genes. The results revealed significant gene rearrangements in Ramaria mitogenomes, including gene displacement and tRNA duplication. Utilizing Bayesian inference and maximum likelihood methods on a comprehensive set of conserved mitochondrial proteins, we generated a well-supported phylogenetic tree for Basidiomycota. This analysis revealed that R. brunneciacina and R. flavescens are closely related, while confirming the paraphyletic nature of the Ramaria genus and its genetic affinity with other species of the subclass Phallomycetidae. This study presents a basic structure for understanding the evolutionary dynamics, genetic makeup, and taxonomy categorization of this significant fungal community.

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基于线粒体基因组分析的三种拉玛属植物系统发育关系

在大型真菌的历史上，拉马利菌一直是一个非凡的属。然而，关于这一大型真菌属的信息缺乏。本研究确定了三种Ramaria物种线粒体基因组（有丝分裂基因组）中核苷酸的顺序，然后对获得的遗传信息进行了详细的调查。brunnecliacina、ichnusensis和R. flavescens的圆形有丝分裂基因组大小分别为78,960、61,851和81,282 bp。这些基因组在遗传含量、基因长度、tRNA和密码子使用方面表现出差异。拉马利亚有丝基因组在几个蛋白质编码基因中表现出可变的进化速率。结果显示，Ramaria有丝分裂基因组中存在显著的基因重排，包括基因位移和tRNA重复。利用贝叶斯推理和最大似然方法对一组完整的保守线粒体蛋白，我们生成了一个很好的支持担子菌门的系统发育树。结果表明，brunneciacina与R. flavescens亲缘关系较近，同时证实了Ramaria属的副葡萄性及其与其他菌科物种的亲缘关系。本研究为了解这一重要真菌群落的进化动力学、遗传组成和分类分类提供了一个基本结构。

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来源期刊

Ecology and Evolution ECOLOGY-

CiteScore

4.40

自引率

3.80%

发文量

1027

审稿时长

3-6 weeks

期刊介绍： Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment. Ecology and Evolution gives prompt and equal consideration to papers reporting theoretical, experimental, applied and descriptive work in terrestrial and aquatic environments. The journal will consider submissions across taxa in areas including but not limited to micro and macro ecological and evolutionary processes, characteristics of and interactions between individuals, populations, communities and the environment, physiological responses to environmental change, population genetics and phylogenetics, relatedness and kin selection, life histories, systematics and taxonomy, conservation genetics, extinction, speciation, adaption, behaviour, biodiversity, species abundance, macroecology, population and ecosystem dynamics, and conservation policy.