Nanopore sequencing: flourishing in its teenage years

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT As one of the most threatened mammalian taxa, lemurs Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on genomics to identify populations particular concern. However, many these genomic approaches necessitate high‐quality genomes. While advent next‐generation sequencing technologies and resulting reduction in associated costs led proliferation data reference genomes, global discrepancies capabilities often result biological samples from biodiverse host countries being exported facilities Global North, creating inequalities access training within research. Here, we present first published genome for endangered red‐fronted brown lemur ( Eulemur rufifrons ) efforts conducted entirely country using portable Oxford Nanopore sequencing. Using an archived E. specimen, long‐read, nanopore at Centre ValBio Research Station near Ranomafana National Park, rural Madagascar, generating over 750 Gb 10 MinION flow cells. Exclusively this long‐read data, assembled 2.157 gigabase, 2980‐contig nuclear assembly with N50 101.6 Mb a 17,108 bp mitogenome. The had 30× average coverage was comparable completeness other primate 96.1% BUSCO score primate‐specific genes. only annotated available speciose genus, resource will prove vital studies while our exhibit potential protocol research build capacity.

Language: Английский

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Sequencing and Assembling the Genome of Przewalski's Horse in the Classroom

Journal of Equine Veterinary Science, Journal Year: 2025, Volume and Issue: 147, P. 105383 - 105383

Published: Feb. 16, 2025

Language: Английский

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Statistical framework for calling allelic imbalance in high-throughput sequencing data

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 18, 2025

High-throughput sequencing facilitates large-scale studies of gene regulation and allows tracing the associations individual genomic variants with changes in expression. Compared to classic association studies, assessment an allelic imbalance at heterozygous captures functional variant effects smaller sample sizes, higher sensitivity, better resolution. Yet, identification allele-specific from read counts remains challenging due data-dependent biases overdispersion arising technical biological variability. We present MIXALIME, a novel computational framework for calling diverse omics data repertoire statistical models accounting mapping bias copy number variation. benchmark MIXALIME DNase-Seq, ATAC-Seq, CAGE-Seq data, we demonstrate that highlights causal GWAS results. Finally, as showcase practical application atlas exhibiting chromatin accessibility, built thousands available datasets obtained cell types. The authors identify variants, i.e., single nucleotide allele-specificity (allelic imbalance) any type assay. Application this yields altering

Language: Английский

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The genome of Przewalski’s horse (Equus ferus przewalskii)

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(8)

Published: May 28, 2024

Abstract The Przewalski’s horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in wild multiple conservation efforts convened preserve species, including captive breeding programs, reintroduction and monitoring systems, protected lands, cloning. Availability a highly contiguous reference genome essential support these continued efforts. We used Oxford Nanopore sequencing produce scaffold-level 2.5 Gb nuclear assembly 16,002 bp mitogenome from mare. All drafts were generated 111 sequence single PromethION R10.4.1 flow cell. contained 37 genes standard mammalian configuration was 99.63% identical domestic caballus). assembly, EquPr2, 2,146 scaffolds with N50 85.1 Mb, 43X mean depth, BUSCO quality score 98.92%. EquPr2 successfully improves upon existing (Burgud), 25-fold fewer scaffolds, 166-fold larger N50, phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation 2.1% hydroxymethylation globally. Allele-specific analysis between pseudohaplotypes 226 differentially methylated regions known imprinted loci not previously reported as imprinted. heterozygosity rate 0.165% matches previous estimates for species compares favorably other animals. This improved will serve valuable resource comparative genomics investigations.

Language: Английский

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Statistical framework for calling allelic imbalance in high-throughput sequencing data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 9, 2023

Abstract High-throughput sequencing facilitates large-scale studies of gene regulation and allows tracing the associations individual genomic variants with changes in expression. Compared to classic association studies, allelic imbalance at heterozygous captures functional effects regulatory genome variation smaller sample sizes higher sensitivity. Yet, identification allele-specific events from read counts remains non-trivial due multiple sources technical biological variability, which induce data-dependent biases overdispersion. Here we present MIXALIME, a novel computational framework for calling diverse omics data repertoire statistical models accounting mapping bias copy-number variation. We benchmark MIXALIME against existing tools demonstrate its practical usage by constructing an atlas chromatin accessibility, UDACHA, thousands available datasets obtained cell types. Availability https://github.com/autosome-ru/MixALime , https://udacha.autosome.org

Language: Английский

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The genome of Przewalski’s horse (Equus ferus przewalskii)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 21, 2024

Abstract The Przewalski’s horse ( Equus ferus przewalskii ) is an endangered equid native to the steppes of central Asia. After becoming extinct in wild, multiple conservation efforts convened preserve species including captive breeding programs, reintroduction and monitoring systems, protected lands, cloning. Availability a highly contiguous reference genome essential support these continued efforts. We used Oxford Nanopore sequencing produce scaffold-level 2.5 Gb nuclear assembly 16,002 bp mitogenome from mare. All drafts were generated 111 sequence single PromethION R10.4.1 flow cell. contained 37 genes standard mammalian configuration was 99.63% identical domestic caballus ). assembly, EquPr2, 2,146 scaffolds with N50 85.1 Mb, 43X mean depth, BUSCO quality score 98.92%. EquPr2 successfully improves upon existing (Burgud), 25-fold fewer scaffolds, 166-fold larger N50, phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation 2.1% hydroxymethylation globally. Allele-specific analysis between pseudohaplotypes 226 differentially methylated regions (DMRs) known imprinted loci not previously reported as imprinted. heterozygosity rate 0.165% matches previous estimates for compares favorably other animals. This improved will serve valuable resource comparative genomics investigations.

Language: Английский

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Overcoming Limitations to Deep Learning in Domesticated Animals with TrioTrain

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 20, 2024

ABSTRACT Variant calling across diverse species remains challenging as most bioinformatics tools default to assumptions based on human genomes. DeepVariant (DV) excels without joint genotyping while offering fewer implementation barriers. However, the growing appeal of a “universal” algorithm has magnified unknown impacts when used with non-human Here, we use bovine genomes assess limits human-genome-trained models in other species. We introduce first multi-species DV model that achieves lower Mendelian Inheritance Error (MIE) rate during single-sample genotyping. Our novel approach, TrioTrain, automates extending for Genome In A Bottle (GIAB) resources and uses region shuffling mitigate barriers SLURM-based clusters. To offset imperfect truth labels animal genomes, remove discordant variants before training, where are tuned genotype offspring correctly. With cattle, yak, bison trios build 30 iterations five phases. observe remarkable performance phases testing GIAB mean SNP F1 score >0.990. HG002, our phase 4 identifies more at MIE than DeepTrio. F1-hybrid substantially reduces inheritance errors 0.03 percent. Although constrained by labels, find multi-species, trio-based training produces robust variant model. research demonstrates exclusively restricts application deep-learning approaches comparative genomics.

Language: Английский

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De novogenome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 10, 2024

ABSTRACT As one of the most threatened mammalian taxa, lemurs Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on genomics to identify populations particular concern. However, many these genomic approaches necessitate high-quality genomes. While advent next generation sequencing technologies and resulting reduction associated costs led proliferation data reference genomes, global discrepancies in capabilities often result biological samples from biodiverse host countries being exported facilities Global North, creating inequalities access training within research. Here, we present first genome for endangered red-fronted brown lemur ( Eulemur rufifrons ) efforts conducted entirely country using portable Oxford Nanopore sequencing. Using an archived E. specimen, long-read, nanopore at Centre ValBio Research Station near Ranomafana National Park, rural Madagascar, generating over 750 Gb 10 MinION flow cells. Exclusively this long-read data, assembled 2.21 gigabase, 20,330-contig nuclear assembly with N50 98.9 Mb a 17,108 bp mitogenome. The had 31x average coverage was comparable completeness other primate 95.47% BUSCO score primate-specific genes. only annotated available speciose genus, resource will prove vital studies while our exhibit potential protocol research build capacity.

Language: Английский

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Four new genome sequences of the Pallas’s cat (Otocolobus manul): an insight into the patterns of within-species variability

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 9, 2024

Manul (

Language: Английский

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