Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism. We are submitting sex-seperated H4K16ac ChIP-seq datasets from D. busckii and D. virilis that were processed on our D. busckii and D. virilis genome assemblies that we are also providing here. For the H4K16ac ChIP-seq samples (2 replicates each) we provide histone 3 (H3) ChIP-seq samples (1 replicate for D. busckii, 2 replicates for D. virilis) as well as input samples (1 replicate for D. busckii, 2 replicates for D. virilis) as controls. We provide bigWig files of mapped reads of individual replicates as well as bigWig files of log2fold ratio input-normalized merged replicates. Processing of these samples was done on our D. busckii and D. virilis assemblies which we provide as fastq files. Raw data for generating both assemblies is deposited in SRA (SRR7029387-SRR7029398).

我们采用结合PacBio数据与已发表的Illumina测序读段的方法，对布氏果蝇（D. busckii）进行从头组装，获得其重叠群（contig）。我们从布氏果蝇胚胎中获取Hi-C数据，将这些重叠群锚定至染色体长度的支架序列（scaffold）。针对维氏果蝇（D. virilis），我们同样生成Hi-C数据，将已发表的Dvir_caf1支架序列排序并定向，构建为染色体长度的基因组组装版本。此外，我们以黑腹果蝇（D. melanogaster）为参照，比较这两个新组装版本的Hi-C相互作用矩阵，分析其同线性区块（synteny block）与作为全染色体基因调控机制的剂量补偿现象。我们将提交基于本研究组装的布氏果蝇与维氏果蝇基因组，配套提供二者的分性别组蛋白H4赖氨酸16乙酰化（H4K16ac）染色质免疫共沉淀测序（ChIP-seq）数据集。针对每组各含2个生物学重复的H4K16ac ChIP-seq样本，我们同时提供组蛋白H3（H3）ChIP-seq样本（布氏果蝇1个生物学重复，维氏果蝇2个生物学重复）以及输入对照样本（布氏果蝇1个生物学重复，维氏果蝇2个生物学重复）作为对照。我们提供单个重复样本比对读段的bigWig格式文件，以及经输入样本标准化后的合并重复样本log2倍数变化比值的bigWig格式文件。本研究所有样本的处理均基于我们组装的布氏果蝇与维氏果蝇基因组，相关FASTQ格式文件也一并提供。用于构建这两个基因组组装版本的原始数据已提交至序列读取档案（SRA），编号为SRR7029387-SRR7029398。