Project description:Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on a single assembly to represent a species. We aligned 20 telomere-to-telomere (T2T) assemblies spanning great ape evolution and variation to define 1,596 consensus human ancestor quickly evolved regions (Consensus HAQERs), regions that diverged rapidly between the human-chimpanzee ancestor and an ancestral node of modern humans. Unlike prior HAQER sets based on single assemblies for a species, Consensus HAQERs incorporate population variation, reducing the likelihood of intraspecies variation appearing to be interspecies divergence. These regions contain signatures of elevated mutation rates, ancient positive selection, bivalent regulatory function, and are enriched in disease-linked loci, often emerging in previously inaccessible repetitive DNA. Through multiplex, single-cell enhancer assays, we identify HAQERs as active enhancers in the developing brain and cardiomyocytes, highlighting their potential contributions to human-specific gene regulation.

2025-11-29 | GSE311407 | GEO

Ludwigia sequencing plastome data

Project description:Ludwigia grandiflora subsp. hexapetala and Ludwigia peploides subsp. montevidensis plastome reads

| PRJEB83105 | ENA

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

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.

2019-10-14 | GSE120750 | GEO

SGG assemblies

Project description:de novo assemblies of streptococcus gallolyticus gallolyticus

| PRJEB88997 | ENA

The genomes of the ancestral species of peanut - a remarkable case of living archaeology

Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaÃ«nsis). We show they are similar to the peanutâs A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanutâs component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaÃ«nsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut. Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.

2016-07-03 | E-GEOD-71357 | biostudies-arrayexpress

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