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.

本研究对模式生物莱茵衣藻（Chlamydomonas reinhardtii）的12株野外分离株与8株常用实验室菌株开展全基因组重测序，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。本研究数据验证了此前的研究结论，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%，且在北美地区呈现地理群体结构，同时存在采样位点间的基因混合迹象。对野外分离株中预测的功能丧失型突变的分析显示，参与核心细胞功能的基因较为保守；而大型基因家族及功能注释不足的基因，则更易出现具有重大效应的突变。对未比对上参考基因组的序列读段（reads）进行从头组装后，从野外分离株中鉴定出了CC-503参考组装基因组中不存在的基因。实验室参考菌株的基因组多态性模式，与其起源于二倍体接合孢子的重组后代这一背景相符。大片段重复或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。丰富的自然变异为莱茵衣藻研究提供了全新的遗传多样性资源，其中包含的天然等位基因，有望在基因功能研究及数量遗传性状解析中发挥重要作用。