RT Journal Article
SR Electronic
T1 Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 867879
DO 10.1101/867879
A1 Samuel Whiteford
A1 Arjen E. van’t Hof
A1 Ritesh Krishna
A1 Thea Marubbi
A1 Stephanie Widdison
A1 Ilik J. Saccheri
A1 Marcus Guest
A1 Neil I. Morrison
A1 Alistair C. Darby
YR 2019
UL http://biorxiv.org/content/early/2019/12/06/867879.abstract
AB 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.