Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

G3 : Genes - Genomes - Genetics
Edwin A SolaresR Scott Hawley

Abstract

Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly...Continue Reading

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Citations

May 28, 2019·Genome Research·Jun YoshimuraErich M Schwarz
Jan 24, 2020·G3 : Genes - Genomes - Genetics·Ryan BracewellDoris Bachtrog
May 16, 2019·PLoS Biology·Ching-Ho ChangBarbara G Mellone
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Mar 29, 2020·G3 : Genes - Genomes - Genetics·Ahmed MajekodunmiWilliam D Gilliland
Nov 17, 2020·Frontiers in Plant Science·Paolo Baldi, Nicola La Porta
Feb 11, 2021·Genome Research·Mahul ChakrabortyJ J Emerson
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Jun 1, 2021·Frontiers in Microbiology·Hooi-Leng SerLearn-Han Lee
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Jul 20, 2021·ELife·Bernard Y KimDmitri A Petrov
Jun 29, 2021·Molecular Ecology Resources·Filip WierzbickiRobert Kofler
Dec 7, 2021·G3 : Genes - Genomes - Genetics·Shane D WidanagamaAaron B A Shafer

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Methods Mentioned

BETA
genotyping
Illumina sequencing
Chicken

Software Mentioned

Con
Canu
mummerplot
ggplot
MITOS
nanopolish
QUAST
Bowtie
PBDAG
miniasm

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