The SFI Centre for Research Training in Genomics Data Sciences, National University of Ireland Galway, Galway, Republic of Ireland.
Department of Public Health and Primary Care, School of Medicine, Trinity College Dublin, Dublin, Republic of Ireland.
Yeast. 2022 Jan;39(1-2):83-94. doi: 10.1002/yea.3689. Epub 2022 Jan 12.
Fission yeast is an important model organism in evolutionary genetics and cell biology research. Nevertheless, most research is limited to a single laboratory strain and knowledge of its natural occurrence is limited, which reduces our understanding of its life history and hinders isolation of new strains from nature. Understanding the natural diversity of fission yeast can provide insight into its genetic and phenotypic diversity and the evolutionary processes that shaped these. Here, we aimed to identify candidate natural habitats of fission yeasts by searching through a large collection of publicly available environmental metatranscriptomic datasets. Using a custom pipeline, we processed over 13,000 NCBI SRA accessions, from a wide range of 34 different environmental categories. Overall, we found a very low abundance of putative yeast transcripts, with most fission yeast signatures coming from the categories of 'food' and 'terrestrial arthropods'. Additionally, a signal could be found in a variety of marine and fresh aquatic habitats. Our results do not provide a conclusive answer on the natural habitat of fission yeasts, but our analysis further narrows the range of locations where fission yeasts naturally occur.
裂殖酵母是进化遗传学和细胞生物学研究中的重要模式生物。然而，大多数研究仅限于单一的实验室菌株，对其自然发生的了解有限，这限制了我们对其生活史的理解，并阻碍了从自然界中分离新菌株。了解裂殖酵母的自然多样性可以深入了解其遗传和表型多样性以及塑造这些多样性的进化过程。在这里，我们旨在通过搜索大量公开可用的环境宏转录组数据集来确定裂殖酵母的候选自然栖息地。使用自定义管道，我们处理了来自 34 个不同环境类别的超过 13000 个 NCBI SRA 访问号。总的来说，我们发现了非常低丰度的假定酵母转录本，大多数裂殖酵母特征来自“食物”和“陆地节肢动物”类别。此外，还可以在各种海洋和淡水生境中发现信号。我们的结果并没有为裂殖酵母的自然栖息地提供一个明确的答案，但我们的分析进一步缩小了裂殖酵母自然发生的地点范围。
