Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)
Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)
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DOI：
10.1093/gbe/evz171
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发表时间：
2019-08
影响因子：
3.3
通讯作者：
Stephan Majda;J. Boenigk;D. Beisser
中科院分区：
文献类型：
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作者：
Stephan Majda;J. Boenigk;D. Beisser
摘要原生生物个体小、不易观察、形态特征差，而目前的系统发育分析方法仅使用少量的标记基因来测量遗传多样性，因此原生生物的物种划分仍是一个挑战。为了解决这个问题，我们评估的原生生物Poteriospumella lacustris，第一个自由生活的，非模式生物研究全基因组种内变异的菌株的基因组水平的分歧和微进化。湖生泡孔菌（Poteriospumella lacustris）是一种淡水原生生物，属于绿藻纲，广泛分布于世界各地。我们通过使用Illumina和PacBio平台对来自不同地理区域（新西兰，中国和奥地利）的三种菌株的基因组进行测序。组装的基因组很小，只有49 - 55 Mb，但基因丰富，有16，000 - 19，000个基因，其中18，000个基因可以分配到功能类别。这些基因中至少有68%是这三个物种共有的。遗传变异主要发生在可能参与生态位适应的基因中。最令人惊讶的是，我们检测到菌株之间的基因组倍性差异（二倍体、三倍体和四倍体）。在分析种内变异时，确定了多种多样性机制，包括SNP、倍性变化和基因组大小减小。
Abstract Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation. Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution. We examined three strains from different geographic regions (New Zealand, China, and Austria) by sequencing their genomes with the Illumina and PacBio platforms. The assembled genomes were small with 49–55 Mb but gene-rich with 16,000–19,000 genes, of which ∼8,000 genes could be assigned to functional categories. At least 68% of these genes were shared by all three species. Genetic variation occurred predominantly in genes presumably involved in ecological niche adaptation. Most surprisingly, we detected differences in genome ploidy between the strains (diploidy, triploidy, and tetraploidy). In analyzing intraspecific variation, several mechanisms of diversification were identified including SNPs, change of ploidy and genome size reduction.