División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí 78216, Mexico.
Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36824, Mexico.
G3 (Bethesda). 2021 Jul 14;11(7). doi: 10.1093/g3journal/jkab088.
Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome.
拉格啤酒是由杂交酿酒酵母（Saccharomyces pastorianus）制成的。由于难以组装杂种基因组，例如来自双亲类型的同源染色体的存在，以及它们之间的易位，许多公开可用的 S. pastorianus 基因组组装体高度碎片化。为了改进先前测序的拉格酵母杂种 Saccharomyces sp. 790 的组装，并阐明其基因组结构，我们提出了使用替代实验证据的方法。我们确定了 Saccharomyces sp. 790 的系统发育位置，并将其确立为 S. pastorianus 790。然后，我们从该酵母中获得了带有 BAC 末端序列（BES）的细菌人工染色体（BAC）基因组文库。为了分析这些数据，我们开发了一个流水线（适用于其他组装体），根据其取向对 BES 对的比对进行分类。对于 S. pastorianus 790 的情况，成对的 BES 比对验证了部分组装体，不成对的 BES 比对则提示了连续体的连接或错误组装。重要的是，BAC 文库得以保存，并用于验证实验。不成对的 BES 比对用于升级以前的组装体，并提供了易位的改进检测。通过这种方法，我们提出了 S. pastorianus 790 的基因组结构，它与其他拉格酵母的基因组结构相似；然而，当我们估计染色体拷贝数并实验测量其基因组大小时，我们发现一个关键的区别是 S. pastorianus 790 的出色的多倍体水平（allopentaploid）。总之，我们的结果表明，将生物信息学分析与实验数据（如长插入克隆信息）相结合，以改进杂种基因组的短读长组装具有重要价值。
