Data_Sheet_2_The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia.DOCX

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

对地衣真菌共生体的繁殖生物学研究传统上具有挑战性，因其复杂的生活方式。与普遍认为的单倍体观点相悖，一项最近的基因组学研究在Letharia中发现了类似三倍体的信号。在本研究中，我们通过分析纯培养和菌苔中的基因组数据，并对自然种群中的MAT位点进行PCR调查，推断出Letharia的基因组组织和繁殖方式。我们发现，包括源自L. lupina单个有性孢子的纯培养在内的四个Letharia样本的读数计数变化与单倍体一致。相比之下，来自菌苔宏基因组数据的L. lupina读数计数表现出类似三倍体的特征。对交配型位点的表征揭示了该属中保守的异宗配合配置，以及我们所识别的辅助基因。我们发现，北美洲L. vulpina和L. lupina的交配型分布平衡，暗示着广泛的性繁殖，但欧洲L. vulpina的分布则高度倾斜，这与主要的无性繁殖相吻合。综合以上发现，我们提出Letharia真菌为异宗配合且通常为单倍体，并提供证据表明类似三倍体的个体是L. lupina与一个未知的Letharia谱系的杂交种，从而将经典系统学和遗传学研究与最近的基因组观察结果相协调。