Biology subjects

Kolmogorov, M.

Publications and source records attributed to Kolmogorov, M..

5 recordsLinked to original sources

bioRxiv2018

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most widely used inbred strains and reveal for the first time extensive strain-specific haplotype variation. We identify and characterise 2,567 regions on the current Genome Reference Consortium mouse reference genome exhibiting the greatest sequence diversity between strains. These regions are enriched for genes involved in defence and immunity, and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. Several immune related loci, some in previously identified QTLs for disease response have novel haplotypes not present in the reference that may explain the phenotype. We used these genomes to improve the mouse reference genome resulting in the completion of 10 new gene structures, and 62 new coding loci were added to the reference genome annotation. Notably this high quality collection of genomes revealed a previously unannotated gene (Efcab3-like) encoding 5,874 amino acids, one of the largest known in the rodent lineage. Interestingly, Efcab3-like-/- mice exhibit severe size anomalies in four regions of the brain suggesting a mechanism of Efcab3-like regulating brain development.

genomics↗

bioRxiv2018

Culture-free generation of microbial genomes from human and marine microbiomes

Our understanding of natural microbial communities is shaped by the careful investigation of a relatively small number of isolated and cultured organisms, and by analysis of genomic sequences obtained by culture-free metagenomic sequencing approaches. Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire. Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture. Recent molecular techniques that partition long DNA fragments and then barcode short fragments derived from them produce \"read clouds\", which are short-read sequences containing long-range information. Here, we present a novel application of a read cloud technique to microbiome samples, as well as Athena, a de novo assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to sequence human stool samples from two healthy individuals, and compare it to existing short read and synthetic long read metagenomic sequencing approaches. We find that read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts. These genome drafts are also highly contiguous (>200kb N50, <10 contigs), even for bacteria that have relatively low (20x) raw short read sequence coverage. We also apply this approach to a significantly more complex marine sediment sample and obtain 23 genome drafts with valuable 16S ribosomal RNA taxonomic marker sequences, nine of which are complete genome drafts. Read cloud metagenomic sequencing allows culture-free generation of high quality microbial genome drafts using only a single shotgun experiment.

genomics↗

bioRxiv2018

Assembly of Long Error-Prone Reads Using Repeat Graphs

The problem of genome assembly is ultimately linked to the problem of the characterization of all repeat families in a genome as a repeat graph. The key reason the de Bruijn graph emerged as a popular short read assembly approach is because it offered an elegant representation of all repeats in a genome that reveals their mosaic structure. However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat characterization. We present the Flye algorithm for constructing the A-Bruijn (assembly) graph from long error-prone reads, that, in contrast to the k-mer-based de Bruijn graph, assembles genomes using an alignment-based A-Bruijn graph. In difference from existing assemblers, Flye does not attempt to construct accurate contigs (at least at the initial assembly stage) but instead simply generates arbitrary paths in the (unknown) assembly graph and further constructs an assembly graph from these paths. Counter-intuitively, this fast but seemingly reckless approach results in the same graph as the assembly graph constructed from accurate contigs. Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph. We benchmark Flye against several state-of-the-art Single Molecule Sequencing assemblers and demonstrate that it generates better or comparable assemblies for all analyzed datasets.

bioinformatics↗

bioRxiv2017

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

genomics↗

bioRxiv2016

Chromosome assembly of large and complex genomes using multiple references

Despite the rapid development of sequencing technologies, assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout, a reference-assisted assembly tool that now works for large and complex genomes. Taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. Using Ragout, we transformed NGS assemblies of 15 different Mus musculus and one Mus spretus genomes into sets of complete chromosomes, leaving less than 5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long PacBio reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. Additionally, we applied Ragout to Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared to other genomes from the Muridae family. Chromosome color maps confirmed most large-scale rearrangements that Ragout detected.

bioinformatics↗