Daphnia pulex isolate:PA42 Genome sequencing

Although a reference assembly from Illumina reads is available for D. pulex (Ye, et al. 2017), it is still fragmented and contains ~13 million gaps. Moreover, due to the conserved strategy of predicting genes with at least two pieces of evidence, key genes may have been missed in the reference genome. To solve this, we generated an improved assembly of sexual D. pulex using reads from 20 PacBio SMRT cells, with total coverage of 79.4x. The reads were assembled by Canu (Koren, et al. 2017) and further scaffolded with dovetail reads. The draft genome presented here, PA42 4.1, consists of 190 Mb of sequences located on 493 scaffolds. The N50 scaffold size is 1.2 Mb, which increased by 134% compared to the previous assembly. The N50 scaffold number is 36 and the largest scaffold is 7.6 Mb, indicating high integrity of the assembly. Mean scaffold size is 4.5 times and median scaffold size is 17.7 times of the previous assembly. In addition, the genome size has increased by 33.1 Mb and gap size has decreased by 9.4 Mb, which is likely due to repetitive regions in the genome were resolved by the long reads.