Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.

本研究对12株野外分离株与8株经典实验室菌株——均为模式生物莱茵衣藻（Chlamydomonas reinhardtii）——开展全基因组重测序（whole-genome resequencing），旨在解析其基因组多样性，并为自然变异相关研究提供数据资源。本研究数据支持既往研究结论，即莱茵衣藻是真核生物中多样性最高的类群之一。其核苷酸多样性约为3%，在北美地区呈现显著的地理结构分化特征，且不同采样位点间存在一定的遗传混合迹象。对野外分离株中预测功能丧失突变（loss-of-function mutations）的分析显示，参与核心细胞功能的基因呈现进化保守性；而大型基因家族及功能注释不足的基因，则更易发生强效突变（major effect mutations）。对未比对读段（unmapped reads）进行从头组装（de novo assembly）后，我们在野外分离株中发现了CC-503参考基因组组装中缺失的基因。实验室参考菌株的基因组多态性模式，与其起源于二倍体合子孢子（diploid zygospore）的重组后代这一背景相符。大片段复制或基因扩增是实验室菌株的显著特征，且这类变异大概率产生于实验室培养过程中。本研究发掘的大量自然变异，为莱茵衣藻研究提供了全新的遗传多样性资源，其中天然存在的等位基因（alleles）可用于基因功能研究及数量遗传性状的解析。