Extensive hidden genetic variation shapes the structure of functional elements in Drosophila

Abstract

Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, though the fragmented nature of most contemporary assemblies obscure them. To discover such mutations, we assembled the first reference quality genome of Drosophila melanogaster since its initial sequencing. By comparing this genome to the existing D. melanogaster assembly, we create a structural variant map of unprecedented resolution, revealing extensive genetic variation that has remained hidden until now. Many of these variants constitute strong candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that dramatically amplifies the expression of detoxification genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high quality references are to deciphering phenotypes.

The genome ofDrosophila innubilareveals lineage-specific patterns of selection in immune genes

“…We extracted DNA following the protocol described in (Chakraborty et al 2017) for D. 466 innubila, D. falleni and D. phalerata as further described in the supplementary materials. We 467 prepared the D. innubila DNA as a sequencing library using the Oxford Nanopore Technologies 468 we evaluated the quality of the genome and the extent of improvement in quality, by calculating 494 the N50 and using BUSCO to identify the presence of conserved genes in the genome, from a 495 database of 2799 single copy Dipteran genes (Simão et al 2015).…”

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

“…However, with the advent of long-read sequencing and other technologies that capture long-range linkage information, we are now able to study the effects of larger mutational events such segmental duplications, deletions and other complex structural variants (e.g. Chakraborty et al 2018;Kronenberg et al 2018). Chromosomes may undergo extensive rearrangement via inversions, translocations, fusions and fissions (Eichler and Sankoff 2003).…”

Improved genome assembly and annotation of the soybean aphid (Aphis glycinesMatsumura)

“…Furthermore, although highly contiguous assemblies have recently been published for two aphid species (Jiang et al 2019;Chen et al 2019), the majority of publicly available aphid genomes were sequenced using second-generation short-read sequencing technology, resulting in fragmented assemblies that contain thousands of genomic scaffolds. Although these assemblies may be accurate at the gene-level, and have facilitated many important discoveries, they likely underrepresent repetitive genome content (Treangen and Salzberg 2012;Sedlazeck et al 2018) and may be unsuitable for analyses such as the detection of largescale structural variants (Chaisson et al 2015;Chakraborty et al 2017) and genome-wide synteny analysis (Liu et al 2018). To gain a fuller understanding of aphid evolution and adaptation many more high-quality genomes are required.…”