Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
European Molecular Biology Laboratory (EMBL) Hamburg, c/o German Electron Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany.
Sci Data. 2017 Oct 10;4:170149. doi: 10.1038/sdata.2017.149.
The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.
耐寒硅藻脆杆藻的基因组以高度分化的单倍型为特征，这些单倍型散布在其纯合基因组中。在这里，我们描述了如何将 PacBio DNA 和 Illumina RNA 测序相结合，局部地将这种复杂的基因组景观解析为高度分化的单倍型，以及如何将各种环境控制的转录本映射到单个单倍型上。我们使用 FALCON 组装器组装了 PacBio 序列数据，并使用已测序的 F. cylindrus 基因组的注释创建了组装的单倍型解析注释。来自六个不同生长条件的 RNA-seq 数据集用于解析 F. cylindrus 中特定等位基因的基因表达。这种方法可用于研究复杂基因组景观中等位基因的差异表达，并为研究二倍体生物中的分化单倍型如何用于适应和进化高度变化的环境提供了有用的工具。
