@article {Whiteford867879, author = {Samuel Whiteford and Arjen E. van{\textquoteright}t Hof and Ritesh Krishna and Thea Marubbi and Stephanie Widdison and Ilik J. Saccheri and Marcus Guest and Neil I. Morrison and Alistair C. Darby}, title = {Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)}, elocation-id = {867879}, year = {2019}, doi = {10.1101/867879}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Background Recent advances in genomics have addressed the challenge that divergent haplotypes pose to the reconstruction of haploid genomes. However for many organisms, the sequencing of either field-caught individuals or a pool of heterogeneous individuals is still the only practical option. Here we present methodological approaches to achieve three outcomes from pooled long read sequencing: the generation of a contiguous haploid reference sequence, the sequences of heterozygous haplotypes; and reconstructed genomic sequences of individuals related to the pooled material.Results PacBio long read sequencing, Dovetail Hi-C scaffolding and linkage map integration yielded a haploid chromosome-level assembly for the diamondback moth (Plutella xylostella), a global pest of Brassica crops, from a pool of related individuals. The final assembly consisted of 573 scaffolds, with a total assembly size of 343.6Mbp a scaffold N50 value of 11.3Mbp (limited by chromosome size) and a maximum scaffold size of 14.4Mbp. This assembly was then integrated with an existing RAD-seq linkage map, anchoring 95\% of the assembled sequence to defined chromosomal positions.Conclusions We describe an approach to resolve divergent haplotype sequences and describe multiple validation approaches. We also reconstruct individual genomes from pooled long-reads, by applying a recently developed k-mer binning method.}, URL = {https://www.biorxiv.org/content/early/2019/12/06/867879}, eprint = {https://www.biorxiv.org/content/early/2019/12/06/867879.full.pdf}, journal = {bioRxiv} }