Strong sequencing bias in Nanopore and PacBio prevents assembly of Drosophila melanogaster Y-linked genes

Nanopore and PacBio are generally considered free from sequence composition bias, a key factor - alongside read length - that explains their success in producing high quality genome assemblies. However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw reads produced by deep sequencing with state-of-the-art Nanopore (10.4 flow cells, 200x coverage) and PacBio (HiFi 50x). The same exons are accurately assembled using Illumina 65x coverage. We found that these missing exons are consistently located near simple satellite sequences, where sequencing fails at multiple levels: read initiation (very few reads start within satellite regions), read elongation (satellite-containing reads are shorter on average), and base-calling (quality scores drop as sequencing enters a satellite sequence). These findings challenge the assumption that long-read technologies is unbiased and reveal a critical barrier to assembling sequences near repetitive regions. As large-scale sequencing projects move towards telomere-to-telomere assemblies in a wide range of organisms, recognizing and addressing these biases will be important to achieving truly complete and accurate genomes. Additionally, the underrepresented Y-linked exons provides a valuable benchmark for refining those sequencing technologies while improving the assembly of the highly heterochromatic and often neglected Drosophila Y chromosome.