De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture.

ABSTRACT: While short-read sequencing technology has resulted in a sharp increase in the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose the largest challenge for reference genome assembly, and pericentromeric regions and the repeat-rich Y chromosome are typically ignored from sequencing projects. Here, we assemble the genome of Drosophila miranda using long reads for contig formation, chromatin interaction maps for scaffolding and short reads, and optical mapping and bacterial artificial chromosome (BAC) clone sequencing for consensus validation. Our assembly recovers entire chromosomes and contains large fractions of repetitive DNA, including about 41.5 Mb of pericentromeric and telomeric regions, and >100 Mb of the recently formed highly re

SUBMITTER: Mahajan S 

PROVIDER: S-EPMC6117089 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature