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 repetitive neo-Y chromosome. While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold because of the accumulation of repetitive sequences. Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome.

Recurrent gene amplification on Drosophila Y chromosomes suggests cryptic sex chromosome drive is common on young sex chromosomes

“…GAPsec suggest that they may be involved in meiotic conflicts in several members of the pseudoobscura species group. We used high--quality PacBio genome assemblies for two additional members of that species group [33], D. miranda, which diverged form D. pseudoobscura about 2--4 MY ago, and D. athabasca, which diverged 10--15 MY ago [34]. While our Illumina sequencing--based approach failed to detect co--amplified X and Y genes in these species (see Table 1), examination of the assembled PacBio genomes revealed that both gene pairs independently amplified on the sex chromosomes of both D. miranda and D. athabasca (see Figure 5).…”

“…Co--amplification of X/Y genes, on the other hand, is difficult to explain under scenarios that do not involve meiotic conflict: The repeat content of X chromosomes is comparable to that of autosomes [33]; natural selection efficiently purges deleterious mutations from the recombining X; and transcription of the X chromosome in Drosophila males is increased, rather than reduced [42]. Most importantly, co--amplified X and Y genes are enriched for meiosis functions (see also [43]), and the X--linked copies of co--amplified genes are highly expressed in testis [43].…”

“…Indeed, about 1/3 of the co--amplified X/Y genes that we identified in D. miranda did not have an ortholog in D. melanogaster [43]. Finally, we required X--linked co--amplified gene copies to be present in our Illumina assemblies; however, recent gene duplicates are often collapsed is such assemblies [33].…”

Long-read based assembly and annotation of a Drosophila simulans genome

“…This merged assembly encompassed 127.41 Mb on 305 contigs, with a N50 of 5.38 Mb. Interestingly, the merged assembly was only marginally better in terms of contiguity and total size, while bigger improvement is usually observed with this tool (e.g., Chakraborty et al 2016;Mahajan et al 2018). This would be expected if both assemblies were already fairly similar, as suggested by their statistics.…”

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

“…Genome assemblies using long read sequencing have been generated for at least 18 Drosophila species (Allen, Delaney, Kopp, & Chenoweth, n.d.;Bracewell, Chatla, Nalley, & Bachtrog, 2019;Mahajan, Wei, Nalley, Gibilisco, & Bachtrog, 2018;Miller, Staber, Zeitlinger, & Hawley, 2018).Somewhat surprisingly given its economic importance, D.…”