Chinese hamster genome sequenced from sorted chromosomes

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…In two independent previous attempts, the Chinese hamster genome was generated using Illumina sequencing from DNA isolated from liver tissue acquired from the same hamster colony as used for deriving CHO cells in 1957 [Brinkrolf et al, 2013], [Lewis et al, 2013]. The current RefSeq assembly originated from whole-genome libraries with varying insert sizes [Lewis et al, 2013].…”

“…The current RefSeq assembly originated from whole-genome libraries with varying insert sizes [Lewis et al, 2013]. A second assembly (CSA) using chromosome sorted sequencing libraries is also publicly available [Brinkrolf et al, 2013]. The different libraries combined yielded about two billion read pairs with read lengths from 99 to 150 bp, in total 442.22 Gb (see Supplementary material for details).…”

“…However, the longer PacBio SMRT reads and the larger Illumina insert libraries should provide unique strengths that could be captured through assembly merging. Therefore, we aligned the scaffolds and contigs from four independent assemblies: the Illumina-based chromosome sorted assembly (CSA) [Brinkrolf et al, 2013], the RefSeq assembly [Lewis et al, 2013], the pooled Illumina assembly developed here, and our de novo uncurated PacBio SMRT assembly. The Metassembler tool [Wences and Schatz, 2015] uses the first assembly provided as the base and subsequently merges additional assemblies.…”

“…We mapped the sequences between the mouse transcription start site (TSS) to transcription end site (TES) against the PICR metassembly, the RefSeq assembly, and the CSA [Lewis et al, 2013], [Brinkrolf et al, 2013]. Genes were called present if both the TSS and TES were found on the same scaffold.…”

“…The corresponding sequences in PICR were elongated to include UTRs, 5 kb upstream, and 1.5 kb downstream, to capture potential regulatory regions such as promoters or repressive elements. These elongated sequences were mapped against the previously published Chinese hamster genomes [Lewis et al, 2013], [Brinkrolf et al, 2013] and again checked for presence on a single scaffold (Figure 2.d). …”