Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the g...基因组的异染色质区域（heterochromatic regions）富含重复序列且蛋白质编码基因匮乏，因此即便在最优的基因组组装结果中，这类区域也常存在覆盖缺失的情况。基因组中最难完成组装的区域之一为性限染色体。黑腹果蝇（Drosophila melanogaster）的Y染色体完全属于异染色质，却对雄性生育力、适合度及全基因组基因表达具有广泛影响。此类表型变异的遗传基础难以研究，部分原因在于我们尚未明确Y染色体的精细组织架构。为研究黑腹果蝇的Y染色体组织模式，我们开发了一套组装策略：通过虚拟富集异染色质长单分子测序读段（long single-molecule reads），并利用这些读段完成异染色质序列的靶向从头组装。我们借助Illumina测序读段（Illumina reads）识别雄性特异性序列，以此将重叠群（contigs）锚定至Y染色体。我们的分析流程将黑腹果蝇参考基因组延伸了11.9兆碱基对（Mb），填补了43.8%的...