Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.
Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
Mycopathologia. 2019 Apr;184(2):195-212. doi: 10.1007/s11046-019-00328-9. Epub 2019 Mar 19.
The Cryptococcus neoformans species complex is a model organism for fungal studies. Many studies have used two strains, JEC20 and JEC21, and their derivatives. These two strains were obtained through 10 rounds of backcrosses and have been assumed near identical except at the mating-type locus. Here we obtained and compared the JEC20 genome sequence with the published "JEC21" genome. Our comparison revealed 5322 single nucleotide polymorphisms (SNPs) with the majority (N = 3816, 71.7%) located in three genomic regions, including the previously noted mating-type region. The remaining 1506 SNPs (28.3%) were distributed throughout all 14 chromosomes, predominantly at chromosomal ends. To study the potential effects of these three SNP-rich regions on phenotypes, 24 progenies from the JEC20 × JEC21 cross representing eight recombinant genotypes were analyzed for their mating ability, melanin production, capsule formation, and growths at 30 °C and 40 °C. Significant phenotypic variations were found among the progeny. However, the observed phenotypic variations could not be explained by the three SNP-rich regions. Further genome sequencing of our JEC21 and the 24 progenies revealed only six segregating SNPs outside of the three SNP-rich regions between JEC20 and JEC21, a result indicating that the 1500 SNPs identified in the published "JEC21" genome might be caused by sequencing errors and/or strain mixing. However, the six SNPs and the three SNP-rich regions could not explain the observed phenotypic variations. Our analyses suggest that spontaneous mutations accumulated under laboratory conditions could have significant effects on phenotypes and on our interpretations of experimental results.
新生隐球菌种复合体是真菌研究的模式生物。许多研究使用了两个菌株，JEC20 和 JEC21 及其衍生菌株。这两个菌株通过 10 轮回交获得，除交配型位点外，被认为几乎完全相同。在这里，我们获得并比较了 JEC20 基因组序列与已发表的“JEC21”基因组。我们的比较显示，有 5322 个单核苷酸多态性（SNP），其中大多数（N=3816，71.7%）位于三个基因组区域，包括先前提到的交配型区域。其余 1506 个 SNP（28.3%）分布在所有 14 条染色体上，主要位于染色体末端。为了研究这三个 SNP 丰富区域对表型的潜在影响，我们分析了 JEC20×JEC21 杂交的 24 个后代的交配能力、黑色素产生、荚膜形成以及在 30°C 和 40°C 下的生长情况，它们代表了八种重组基因型。在后代中发现了显著的表型变异。然而，观察到的表型变异不能用这三个 SNP 丰富区域来解释。对我们的 JEC21 和 24 个后代的进一步基因组测序仅在 JEC20 和 JEC21 之间的三个 SNP 丰富区域之外发现了六个分离的 SNP，这一结果表明，在已发表的“JEC21”基因组中鉴定的 1500 个 SNP 可能是由测序错误和/或菌株混合引起的。然而，这六个 SNP 和三个 SNP 丰富区域不能解释观察到的表型变异。我们的分析表明，在实验室条件下积累的自发突变可能对表型和我们对实验结果的解释有重大影响。
