The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we ...remapped data from 41 genomes against the T2T reference genome and compared it to the GRCh38 reference. We find a ~ 21% increase in sensitivity improving mapping of 63 inversions on the T2T reference. We identify 26 misorientations within GRCh38 and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. Analysis of 10 additional samples reveals novel rare inversions at chromosomes 15q25.2, 16p11.2, 16q22.1-23.1, and 22q11.21.
There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly ...generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications 35.4%, satellite DNA 22.3%, or regions enriched in GA/AT-rich DNA 27.4%). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.
Abstract
Motivation
Highly contiguous de novo phased diploid genome assemblies are now feasible for large numbers of species and individuals. Methods are needed to validate assembly accuracy and ...detect misassemblies with orthologous sequencing data to allow for confident downstream analyses.
Results
We developed GAVISUNK, an open-source pipeline that detects misassemblies and produces a set of reliable regions genome-wide by assessing concordance of distances between unique k-mers in Pacific Biosciences high-fidelity assemblies and raw Oxford Nanopore Technologies reads.
Availability and implementation
GAVISUNK is available at https://github.com/pdishuck/GAVISUNK.
Supplementary information
Supplementary data are available at Bioinformatics online.
Obligate insect social parasites evolve traits to effectively locate and then exploit their hosts, whereas hosts have complex social behavioral repertoires, which include sensory recognition to ...reject potential conspecific intruders and heterospecific parasites. While social parasites and host behaviors have been studied extensively, less is known about how their sensory systems function to meet their specific selective pressures. Here, we compare investment in visual and olfactory brain regions in the paper wasp Polistes dominula, and its obligate social parasite P. sulcifer, to explore the links among sensory systems,brain and behavior. Our results show significant relative volumetric differences between these two closely related species, consistent with their very different life histories. Social parasites show proportionally larger optic lobes and central complex to likely navigate long‐distance migrations and unfamiliar landscapes to locate the specific species of hosts they usurp. Contrastingly, hosts have larger antennal lobes and calyces of the mushroom bodies compared with social parasites, as predicted by their sensory means to maintain social cohesion via olfactory signals, allocate colony tasks, forage, and recognize conspecific and heterospecific intruders. Our work suggests how this tradeoff between visual and olfactory brain regions may facilitate different sensory adaptations needed to perform social and foraging tasks by the host, including recognition of parasites, or to fly long distances and successful host localizing by the social parasite.
Brain reconstructions reveal differential investment in sensory brain regions between the obligate social parasite Polistes sulcifer and its host, P. dominula. Social parasites have larger optic lobes (blue), which reflects their visual needs to navigate long distances and locate a host nest. Contrastingly, hosts show large antennal lobes (yellow) and calyces of the mushroom bodies (red), coinciding with the olfactory and sensory processing needs of maintaining colony cohesion, including recognizing conspecific and heterospecific intruders. Scale = 1 mm.
Full text
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size
. As a result, patterns of human centromeric variation and models for ...their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions
. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome
. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
Full text
Available for:
GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
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