Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species DOI
Katarina C. Stuart, Hui Zhen Tan, Annabel Whibley

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

ABSTRACT The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged the management threatened species. functional consequences SVs are more complex than for single nucleotide polymorphisms (SNPs), as typically impact a larger proportion genome due to their size thus may likely contribute load. While impacts SV‐specific genetic load less consequential large populations, interplay between weakened selection stochastic processes means that smaller such those Aotearoa hihi/New Zealand stitchbird ( Notiomystis cincta ), harbour high SV Hihi were once confined remnant population, but have been reestablished into six sanctuaries reserves, often via secondary bottlenecks, resulting low diversity, adaptive potential, inbreeding depression. In this study, we use whole resequencing 30 individuals from Tiritiri Matangi population identify nature distribution both SNPs within small avian population. We find SNP individual mutation only moderately correlated, because arise regions recombination evolutionarily conserved. Finally, leverage long‐term monitoring dataset pedigree fitness data assess loads on fitness, realised had similar negative correlations with lifetime fitness. However, masked metrics, positive significant correlation indicating masking deleterious alleles important SNPs. results study indicate examining neglects aspects intra‐specific variation studying has direct implications linking diversity genomic health inform decisions.

Language: Английский

Analysis and benchmarking of small and large genomic variants across tandem repeats DOI
Adam C. English, Egor Dolzhenko, Helyaneh Ziaei Jam

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: April 26, 2024

Language: Английский

Citations

26
Plant graph-based pangenomics: techniques, applications, and challenges DOI Creative Commons

Zezhen Du,

Jiabao He, Wen‐Biao Jiao

et al.

aBIOTECH, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Abstract Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating molecular breeding crops. Conventional methods analysis typically rely on small variants, such as SNPs indels, use single linear reference genomes, which introduces biases reduces performance highly divergent regions. By integrating level sequences, pangenomes, particularly graph offer a promising solution to these challenges. To date, numerous algorithms been developed constructing pangenome graphs, aligning reads performing variant genotyping based graphs. As demonstrated various plant pangenomic studies, advancements allow detection previously hidden especially structural thereby enhancing applications mapping agronomically important genes. However, noteworthy challenges remain be overcome applying approaches plants. Addressing issues will require development more sophisticated tailored specifically Such improvements contribute scalability this approach, production super-pangenomes, hundreds or even thousands de novo–assembled genomes from one species genus can integrated. This, turn, promote broader pan-omic further advancing our understanding driving innovations crop breeding.

Language: Английский

Citations

0
K-mer analysis of long-read alignment pileups for structural variant genotyping DOI Creative Commons
Adam C. English,

Fabio Cunial,

Ginger Metcalf

et al.

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

Published: April 4, 2025

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for SVs that leverages graphs and k-mer vectors rapidly generate accurate SV genotypes. Benchmarking against the latest datasets shows kanpig achieves single-sample concordance of 82.1%, significantly outperforming existing tools, which average 66.3%. explore kanpig's use multi-sample projects by testing on 47 genetically diverse samples find accurately genotypes complex loci (e.g. neighboring other SVs), produces higher than tools. Kanpig requires only 43 seconds process single sample's 20x long-reads can be run PacBio or Oxford Nanopore long-reads.

Language: Английский

Citations

0
Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs DOI Creative Commons
Siegfried Dubois, Matthias Zytnicki, Claire Lemaitre

et al.

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

Published: Dec. 11, 2024

Abstract Motivation Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming replace a linear reference in wide variety of genomic analyses. The construction graph from collection chromosome-size sequences is difficult task that generally addressed using number heuristics. question arises what extent the method influences resulting graph, and characterization variability. Results We aim characterize differences between derived same set genomes with metric which expresses pinpoint differences. designed pairwise comparison algorithm, establishes edit distance graphs, threading through both graphs. applied our pangenome built yeast human chromosome collections, demonstrate effectively characterizes discordances methods scales real datasets. Availability pancat compare published as free Rust software under AGPL3.0 open source license. Source code documentation available at https://github.com/dubssieg/rs-pancat-compare . Contact [email protected] Supplementary information data online https://doi.org/10.5281/zenodo.10932490 Code replicate figures analysis https://github.com/dubssieg/pancat_paper

Language: Английский

Citations

0
Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species DOI
Katarina C. Stuart, Hui Zhen Tan, Annabel Whibley

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

ABSTRACT The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged the management threatened species. functional consequences SVs are more complex than for single nucleotide polymorphisms (SNPs), as typically impact a larger proportion genome due to their size thus may likely contribute load. While impacts SV‐specific genetic load less consequential large populations, interplay between weakened selection stochastic processes means that smaller such those Aotearoa hihi/New Zealand stitchbird ( Notiomystis cincta ), harbour high SV Hihi were once confined remnant population, but have been reestablished into six sanctuaries reserves, often via secondary bottlenecks, resulting low diversity, adaptive potential, inbreeding depression. In this study, we use whole resequencing 30 individuals from Tiritiri Matangi population identify nature distribution both SNPs within small avian population. We find SNP individual mutation only moderately correlated, because arise regions recombination evolutionarily conserved. Finally, leverage long‐term monitoring dataset pedigree fitness data assess loads on fitness, realised had similar negative correlations with lifetime fitness. However, masked metrics, positive significant correlation indicating masking deleterious alleles important SNPs. results study indicate examining neglects aspects intra‐specific variation studying has direct implications linking diversity genomic health inform decisions.

Language: Английский

Citations

0