Project description: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.
Project description: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.
Project description:Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolve 18 chromosomes per haplotype, providing the first chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ~203 Mb, while M. allii-populina reaches ~416 Mb, with high completeness and strong collinearity between haplotypes.
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
Project description:10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).
Project description:De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Dp3a contains a de novo centromere, which was derived from a euchromatic site on the long arm of chromosome 3 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 350 kb with a high-density gene distribution with low-density of transposons. Here we analyzed the kinetochore complex assembled on the de novo centromere, which revealed that it resembles the native centromeres. Meiotic analyses showed that the Dp3a mini-chromosome formed bi-orientation during meiosis I and could stably transmit through meiosis. We applied next generation sequencing technology to analyze gene transcription, DNA methylation and histone modifications for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. The gene expression level within the Dp3a breakpoints of native chromosome 3 indicated a gene dosage effect due to the additional copy of Dp3a mini-chromosome region in chromosome 3. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. No strand-specific bias of DNA methylation was found at maize native and Dp3a de novo centromeres. H2A-T133 phosphorylation occurs in the CENH3 nucleosome. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences.
