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The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2020-12-30 , DOI: 10.1016/j.csbj.2020.12.041 Peng Wu 1 , Zhijie Bao 2 , Wenying Tu 2 , Lijiao Li 2 , Chuan Xiong 3 , Xin Jin 3 , Ping Li 3 , Mingying Gui 1 , Wenli Huang 3 , Qiang Li 2
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2020-12-30 , DOI: 10.1016/j.csbj.2020.12.041 Peng Wu 1 , Zhijie Bao 2 , Wenying Tu 2 , Lijiao Li 2 , Chuan Xiong 3 , Xin Jin 3 , Ping Li 3 , Mingying Gui 1 , Wenli Huang 3 , Qiang Li 2
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The order Boletales is a group of fungi with complex life styles, which include saprophytic and ectomycorrhizal mushroom-forming fungi. In the present study, the complete mitogenomes of two saprophytic Boletales species, , and , were assembled and compared with mitogenomes of ectomycorrhizal Boletales. Both mitogenomes comprised circular DNA molecules with sizes of 78,350 bp and 79,655 bp, respectively. Comparative mitogenomic analysis indicated that the two saprophytic Boletales species contained more plasmid-derived (7 on average) and unknown functional genes (12 on average) than the four ectomycorrhizal Boletales species previously reported. In addition, the core protein coding genes, and , were found to be subjected to positive selection pressure between some Boletales species. Frequent intron gain/loss events were detected in Boletales and Basidiomycetes, and several novel intron classes were found in two species. A total of 33 introns were detected in , and most were found to have undergone contraction in the mitogenome. Mitochondrial genes of species were found to have undergone large-scale gene rearrangements, and the accumulation of intra-genomic repeats in the mitogenome was considered as one of the main contributing factors. Based on combined mitochondrial gene sets, we obtained a well-supported phylogenetic tree for 76 Basidiomycetes, demonstrating the utility of mitochondrial gene analysis for inferring Basidiomycetes phylogeny. The study served as the first report on the mitogenomes of the family Coniophorineae, which will help to understand the origin and evolution patterns of Boletales species with complex lifestyles.
中文翻译：
两种腐生牛肝菌目（Coniophora）的有丝分裂基因组揭示了内含子动态以及质粒衍生和非保守基因的积累
牛肝菌目是一类生活方式复杂的真菌，包括腐生真菌和外生菌根真菌。在本研究中，组装了两种腐生牛肝菌目物种 和 的完整线粒体基因组，并与外生菌根牛肝菌目的线粒体基因组进行了比较。两种有丝分裂基因组均包含大小分别为 78,350 bp 和 79,655 bp 的环状 DNA 分子。比较线粒体基因组分析表明，与之前报道的四种外生菌根牛肝菌目相比，这两种腐生牛肝菌目物种含有更多的质粒衍生基因（平均 7 个）和未知功能基因（平均 12 个）。此外，核心蛋白编码基因 和 被发现在一些牛肝菌目物种之间受到正选择压力。在牛肝菌目和担子菌纲中检测到频繁的内含子获得/丢失事件，并且在两个物种中发现了几个新的内含子类别。总共检测到33个内含子，大多数被发现在有丝分裂基因组中发生了收缩。人们发现物种的线粒体基因发生了大规模的基因重排，线粒体基因组中基因组内重复的积累被认为是主要影响因素之一。基于组合的线粒体基因集，我们获得了 76 种担子菌的有充分支持的系统发育树，证明了线粒体基因分析在推断担子菌系统发育方面的实用性。该研究是Coniophorineae科线粒体基因组的第一份报告，这将有助于了解具有复杂生活方式的牛肝菌目物种的起源和进化模式。
更新日期：2020-12-30
中文翻译：
两种腐生牛肝菌目（Coniophora）的有丝分裂基因组揭示了内含子动态以及质粒衍生和非保守基因的积累
牛肝菌目是一类生活方式复杂的真菌，包括腐生真菌和外生菌根真菌。在本研究中，组装了两种腐生牛肝菌目物种 和 的完整线粒体基因组，并与外生菌根牛肝菌目的线粒体基因组进行了比较。两种有丝分裂基因组均包含大小分别为 78,350 bp 和 79,655 bp 的环状 DNA 分子。比较线粒体基因组分析表明，与之前报道的四种外生菌根牛肝菌目相比，这两种腐生牛肝菌目物种含有更多的质粒衍生基因（平均 7 个）和未知功能基因（平均 12 个）。此外，核心蛋白编码基因 和 被发现在一些牛肝菌目物种之间受到正选择压力。在牛肝菌目和担子菌纲中检测到频繁的内含子获得/丢失事件，并且在两个物种中发现了几个新的内含子类别。总共检测到33个内含子，大多数被发现在有丝分裂基因组中发生了收缩。人们发现物种的线粒体基因发生了大规模的基因重排，线粒体基因组中基因组内重复的积累被认为是主要影响因素之一。基于组合的线粒体基因集，我们获得了 76 种担子菌的有充分支持的系统发育树，证明了线粒体基因分析在推断担子菌系统发育方面的实用性。该研究是Coniophorineae科线粒体基因组的第一份报告，这将有助于了解具有复杂生活方式的牛肝菌目物种的起源和进化模式。
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