Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies

Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facil...

莱茵衣藻（Chlamydomonas reinhardtii）是光合作用、纤毛研究及生物燃料领域中广为使用的参考模式生物。该领域的多数研究仅采用数十株标准实验室菌株，这些菌株被认为具有共同祖先，但却表现出显著的表型差异。为推动莱茵衣藻相关研究的持续开展，并解析其表型变异的成因，我们通过全基因组重测序（whole-genome resequencing）技术对这些菌株的遗传多样性进行了定位分析。我们在39株常用实验室菌株中，共鉴定出524640个单核苷酸变异（single nucleotide variants）位点与4812个结构变异（structural variants）位点。观测到的总遗传多样性中，近98.2%可归因于两种此前未被识别的交替单倍型（haplotypes）——它们以镶嵌模式分布于现存的实验室菌株中。我们提出，这两种单倍型是两株相对分歧度约为2%的菌株之间祖先杂交事件的遗留产物。这些单倍型模式为每一株菌株构建了独特的指纹图谱，可助力