Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.
Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy063.
The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.
Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.
The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
欧洲山毛榉可以说是中欧最重要的顶极阔叶树种，因其有价值的木材而被广泛种植。在这里，我们报告了来自德国中部凯勒瓦尔德-埃德尔湖国家公园未受干扰林分中一棵 300 年树龄个体（Bhaga）的 542Mb 基因组草图序列。
使用混合组装方法，我们将 Illumina 短插入和长插入文库与长 Pacific Biosciences 读数相结合，获得了 542Mb 的组装基因组大小，与流式细胞术基因组大小估计一致。最大的支架大小为 1.15Mb，N50 长度为 145kb，L50 计数为 983。组装体包含 0.12%的 Ns。使用通用单拷贝同源物（BUSCO）基准测试检索到 94%完整的 BUSCO 基因，这在其他高质量树木草图基因组中处于较好水平。共预测到 62012 个蛋白质编码基因，转录组测序辅助预测。此外，我们还报告了一种从休眠芽中提取高分子量 DNA 的有效方法，通过该方法可以将环境细菌和真菌的污染保持在最低水平。
组装的基因组将成为未来有关山毛榉进化和过去适应气候变化的群体基因组学研究的宝贵资源和参考，并有助于识别耐旱相关基因，以便选择和培育个体，使林业适应欧洲的气候变化。一个不断更新的基因组浏览器和下载页面可从 beechgenome.net 访问，该页面将包含参考个体 Bhaga 的未来基因组版本，因为新的测序方法正在不断发展。
