Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38

Nurses' perceptions of aids and obstacles to the provision of optimal end of life care in ICU

Contains fulltext : 172380.pdf (publisher's version ) (Open Access

Worms Have Feelings, Too: Characterization of a Novel Gene Associated with Sensory Cilia in Caenorhabditis elegans

Cilia are microtubule-based organelles that facilitate a variety of sensory and motility-specific processes. Mutations in genes that encode cilia-specific proteins can manifest as highly devastating diseases, such as polycystic kidney disease and Bardet-Biedl syndrome. In this study, a comparative genomics approach was used to identify ciliary genes that facilitate sensory-specific roles. One gene from this candidate list (encoded at the C05D10.2 locus in the C. elegans genome) was chosen for comprehensive characterization. We discovered that a mutant strain of C. elegans that possesses a deletion mutation within the C05D10.2 coding sequence exhibits a highly penetrant dye-filling defect in phasmid ciliated sensory neurons (CSNs). This phenotype was almost completely rescued by introducing a wild-type copy of the C05D10.2 gene into mutant animals. Additionally, we observed that a translational fusion of the full C05D10.2 coding sequence to green fluorescent protein (GFP) is expressed in anterior and posterior sensory neurons in C. elegans, and specifically localizes to the cilia at the tips of those neurons. Finally, preliminary data obtained from an automated worm-tracking system suggest that mutant worms that lack a functional copy of C05D10.2 roam more than wild-type animals. These combined data strongly suggest a sensory-specific role of C05D10.2 in C. elegans, and are corroborated by evidence that the human homolog of C05D10.2 may be associated with cilia function, as well

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations – the frequencies of C>T, A>G, etc. – will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms

Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"

<p>Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.</p

Poxviruses capture host genes by LINE-1 retrotransposition

Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts