Department of Bioscience, Aarhus University, Ny Munkegade 114, Bldg. 1540, DK-8000 Aarhus C, Denmark.
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
Genomics. 2018 Mar;110(2):75-79. doi: 10.1016/j.ygeno.2017.08.008. Epub 2017 Aug 30.
Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors. A total of 26,134 genes were annotated, with bird species accounting for virtually all BLAST hits. We also estimated the substitution rate in the pink-footed goose, which can be of use in future demographic studies, by using a comparative approach with the genome of the chicken, the mallard and the swan goose. A substitution rate of 1.38×10 per nucleotide per generation was obtained when comparing the genomes of the two closely-related goose species (the pink-footed and the swan goose). Altogether, we provide a valuable tool for future genomic studies aiming at particular genes and regions of the pink-footed goose genome as well as other bird species.
注释基因组可以为物种生物学提供新的视角。我们首次对粉脚雁进行了从头开始的全基因组测序。为了获得高质量的从头组装，我们使用了一种策略，即将一个短插入片段配对末端文库与两个 mate-pair 文库相结合。使用三个不同的组装器对粉脚雁基因组进行了从头组装，随后进行了组装评估，以选择最佳的组装器。对于我们的数据，ALLPATHS-LG 的表现最好，因为组装产生的覆盖了大部分基因组，同时引入的错误最少。总共注释了 26134 个基因，鸟类物种几乎占所有 BLAST 命中的全部。我们还通过与鸡、野鸭和天鹅鹅的基因组进行比较，估计了粉脚雁的替代率，这在未来的人口研究中可能会有用。当比较两种密切相关的鹅种（粉脚雁和天鹅鹅）的基因组时，得到了 1.38×10 个核苷酸/代的替代率。总的来说，我们为未来针对粉脚雁基因组的特定基因和区域以及其他鸟类物种的基因组研究提供了有价值的工具。
