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综合分类学方法揭示了智利酒香酵母（Saccharomyces chiloensis）为一种新发现的物种，来自沿海巴塔哥尼亚地区。

An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia.

机构信息

Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile.

Millennium Institute for Integrative Biology (iBio), Santiago, Chile.

出版信息

PLoS Genet. 2024 Sep 6;20(9):e1011396. doi: 10.1371/journal.pgen.1011396. eCollection 2024 Sep.

DOI:10.1371/journal.pgen.1011396
PMID:39241096
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11410238/
Abstract

Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct Saccharomyces lineage in Nothofagus forests of coastal Patagonia. This lineage, designated Saccharomyces chiloensis sp. nov., exhibits 7% genetic divergence from its sister species S. uvarum, as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent S. uvarum population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to S. uvarum, which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from S. uvarum. In addition, we found unique structural variants between S. chiloensis sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that S. chiloensis sp. nov diverged from S. uvarum in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of S. chiloensis sp. nov. illustrates the uniqueness of Patagonia's coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of S. chiloensis sp. nov. is CBS 18620T.

摘要

由于可供准确物种分配的标记有限，微生物的物种划分具有挑战性。在这里，我们应用了一种综合分类学方法，结合了广泛的采样、基于全基因组序列的分类、表型分析以及种间生殖隔离的评估。我们的工作揭示了在巴塔哥尼亚沿海的诺瑟福克松林中存在一个独特的酿酒酵母谱系。这个谱系被命名为酿酒酵母 chiloensis sp. nov.，通过全基因组测序和种群分析，它与姐妹种酿酒酵母 uvarum 的遗传差异为 7%。南美洲-C（SA-C）沿海巴塔哥尼亚种群形成了一个独特的分支，与以前描述的来自大洋洲的一个分化酿酒酵母 uvarum 种群（AUS，发现于澳大利亚和新西兰）密切相关。我们的物种重新分类得到了支持，SA-C 和 AUS 与酿酒酵母 uvarum 的 Ortho Average Nucleotide Identity（OANI）低至 93%，低于建议的 95%物种划分阈值，表明这是一个独立的进化谱系。杂交孢子活力评估提供了有力的证据，表明 SA-C 和 AUS 与酿酒酵母 uvarum 在生殖上是隔离的。此外，我们还发现了酿酒酵母 chiloensis sp. nov. 谱系之间独特的结构变异，包括大规模染色体易位和倒位，以及独特的表型特征，强调了它们在种内的遗传独特性。我们认为，酿酒酵母 chiloensis sp. nov. 是由于冰川作用而与酿酒酵母 uvarum 发生地理隔离后分化的，随后是冰川后扩散，导致太平洋两岸形成了不同的谱系。酿酒酵母 chiloensis sp. nov. 的发现说明了巴塔哥尼亚沿海生物多样性的独特性，并强调了在物种划分中采用综合分类学方法来揭示隐匿微生物物种的重要性。酿酒酵母 chiloensis sp. nov. 的模式标本为 CBS 18620T。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/4e23d3c87e24/pgen.1011396.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/8e8878c7a980/pgen.1011396.g001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/dccdf1761415/pgen.1011396.g004.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/4e23d3c87e24/pgen.1011396.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/8e8878c7a980/pgen.1011396.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/b52c8168a74b/pgen.1011396.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/b6d766184244/pgen.1011396.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/dccdf1761415/pgen.1011396.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/3aba14ef06cb/pgen.1011396.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e52a/11410238/4e23d3c87e24/pgen.1011396.g006.jpg

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