Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes
Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes
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真菌有丝分裂基因组蛋白质编码基因内含子新命名法的提议
DOI：
10.1186/s43008-019-0015-5
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发表时间：
2019-10-10
期刊：
影响因子：
5.4
通讯作者：
Zhang, Yong-Jie
中科院分区：
文献类型：
--
作者：
Zhang, Shu;Zhang, Yong-Jie
真菌线粒体基因经常被I或II组内含子入侵，这是了解真菌进化的理想标记。当比较不同的真菌有丝分裂基因组时，需要一个线粒体内含子的标准命名法以避免混淆。目前，对于rRNA基因中存在的内含子已经有了一个标准的命名，但对于蛋白质编码基因中存在的内含子还缺乏一个标准的命名。在这项研究中，我们提出了一种新的真菌线粒体蛋白编码基因内含子的命名系统，其基础是(1)宿主学名的三个字母缩写，(2)宿主基因名称，(3)一个大写字母P(代表第I组内含子)，S(代表第II组内含子)，或U(代表未知类型的内含子)，(4)根据产生环孢菌素的真菌Tolypocladium inflatum在宿主基因中的内含子插入位置。通过命名不同门的16个真菌有丝分裂基因组中的内含子，包括基础和高级真菌谱系，证明了所建议的命名是可行的，尽管命名需要稍作调整以适应某些特殊条件。该命名法还有可能命名植物/原生动物/动物线粒体内含子。我们希望未来的研究遵循拟议的命名法，以确保不同研究之间的直接比较。
Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungusTolypocladium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16fungiof differentphyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.