Plant pangenomes for crop improvement, biodiversity and evolution

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(7)

Published: Feb. 7, 2023

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis the unique physiological and ecological traits enabling these species to thrive in diverse habitats remains largely unknown. Additionally, many populations have drastically declined due anthropogenic activities past two centuries, their recovery is a high global conservation priority. We generated analyzed high-quality reference genomes for leatherback ( Dermochelys coriacea ) green Chelonia mydas turtles, representing extant sea turtle families. These are highly syntenic homologous, but localized regions noncollinearity were associated with higher copy numbers immune, zinc-finger, olfactory receptor (OR) genes ORs related waterborne odorants greatly expanded turtles. Our findings suggest divergent evolution key gene families may underlie immunological sensory adaptations assisting navigation, occupancy neritic versus pelagic environments, diet specialization. Reduced collinearity was especially prevalent microchromosomes, greater content, heterozygosity, genetic distances between species, supporting critical role vertebrate evolutionary adaptation. Finally, diversity demographic histories starkly contrasted indicating had low yet stable effective population size, exhibit extremely compared other reptiles, harbor load reinforcing concern persistence under future climate scenarios. provide invaluable resources advancing our understanding best practices imperiled lineage.

Language: Английский

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A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

G3 Genes Genomes Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Abstract Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) HiFi PacBio assemble genome of apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x 36), an outcrossed tetraploid Paniceae grass widely cropped feed livestock tropics. We identified removed between homologous unitigs facilitate their scaffolding employed methods for manual curation rearrangements misassemblies. Our final assembly included four haplotypes 36 chromosomes. found that 18 chromosomes originated diploid U. brizantha other either ruziziensis or decumbens. also chromosomal translocation 5 32, as well evidence pairing exclusively within subgenomes, except homoeologous exchange chromosome 21. results demonstrate haplotype-aware accurately species, making them preferred option over collapsed-haplotype assemblies.

Language: Английский

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Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 5, 2025

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

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Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 15(1), P. 3 - 21

Published: Dec. 11, 2021

The rate of global climate change is projected to outpace the ability many natural populations and species adapt. Assisted migration (AM), which defined as managed movement climate-adapted individuals within or outside ranges, a conservation option improve species' adaptive capacity facilitate persistence. Although biologists have long been using genetic tools increase maintain diversity populations, genomic techniques could add extra benefit in AM that include selectively neutral regions genome. In this review, we first propose framework along with detailed procedures aid collaboration among scientists, agencies, local regional managers during decision-making process genomics-guided AM. We then summarize approaches for applying AM, followed by literature search existing incorporation genomics across taxa. Our initially identified 729 publications, but after filtering returned only 50 empirical studies were either directly applied considered related taxa plants, terrestrial animals, aquatic animals; 42 plants. This demonstrated limited application methods organisms other than so provide further case two examples demonstrate negative impact on non-model how be With rapidly developing sequencing technology accumulating data, expect see more successful applications broadly, biodiversity.

Language: Английский

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Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

Insects, Journal Year: 2023, Volume and Issue: 14(3), P. 255 - 255

Published: March 4, 2023

The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of trees worldwide. Mitigation economic and biodiversity impact it causes an international priority that could be greatly aided by a better understanding its biology genetics. Despite relevance, RPW remains poorly understood, research on management strategies often focuses outdated empirical methods produce sub-optimal results. With development omics approaches in genetic research, new avenues for control are becoming increasingly feasible. For example, engineering become available once species’s target genes well characterized terms their sequence, but also population variability, epistatic interactions, more. In last few years alone, there have been major advances studies RPW. Multiple draft genomes currently available, along with short long-read transcriptomes, metagenomes, which facilitated identification interest to scientific community. This review describes previously applied highlights findings impactful management, emphasizes future opportunities challenges this area research.

Language: Английский

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Benchmarking machine learning robustness in Covid-19 genome sequence classification

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: March 13, 2023

The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount sequence data SARS-CoV-2 genome-millions sequences and counting. This data, while being orders magnitude beyond capacity traditional approaches to understanding diversity, dynamics, evolution viruses, is nonetheless a rich resource for machine learning (ML) as alternatives extracting such important information from these data. It hence utmost importance design framework testing benchmarking robustness ML models. paper makes first effort (to our knowledge) benchmark models by simulating biological with errors. In this paper, we introduce several ways perturb genome mimic error profiles common sequencing platforms Illumina PacBio. We show experiments on wide array that some simulation-based different perturbation budgets are more robust (and accurate) than others specific embedding methods certain noise simulations input sequences. Our may assist researchers properly assessing help them understand behavior virus or avoid possible future pandemics.

Language: Английский

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PanGraph: scalable bacterial pan-genome graph construction

Microbial Genomics, Journal Year: 2023, Volume and Issue: 9(6)

Published: June 6, 2023

The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome well-characterized, but arbitrary, isolate. However, any contains only fraction the microbial pangenome , total set genes observed in given species. Reference-based approaches are thus blind dynamics accessory genome, well variation within gene order and copy number. With widespread usage long-read sequencing, number high-quality, complete assemblies has increased dramatically. In addition pangenomic that focus on sets present different genomes, allow investigations evolution structure order. This latter problem, however, computationally demanding with few tools available shed light these dynamics. Here, we PanGraph Julia-based library command line interface for aligning whole genomes into graph. Each represented path along vertices, which turn encapsulate homologous multiple sequence alignments. resultant data succinctly summarizes population-level nucleotide structural polymorphisms can be exported several common formats either downstream analysis or immediate visualization.

Language: Английский

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Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 5949 - 5965

Published: Aug. 23, 2021

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and content structure of chromosomes. As a result, SVs significant source functional genomic variation, is, variation at regions underpinning phenotype differences, can have effects on individual population fitness. While there increasing opportunities to investigate in threatened species via single nucleotide polymorphism (SNP) data sets, remain understudied despite their potential influence fitness traits conservation interest. In this future-focused Opinion, we contend characterizing offers genomics community an exciting opportunity complement SNP-based approaches enhance recovery. We also leverage existing literature-predominantly human health, agriculture ecoevolutionary biology-to identify for readily consider how integrating these into toolbox may transform way manage some world's most species.

Language: Английский

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Technical considerations in Hi‐C scaffolding and evaluation of chromosome‐scale genome assemblies

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 5923 - 5934

Published: Aug. 25, 2021

The recent development of ecological studies has been fueled by the introduction massive information based on chromosome-scale genome sequences, even for species which genetic linkage is not accessible. This was enabled mainly application Hi-C, a method genome-wide chromosome conformation capture that originally developed investigating long-range interaction chromatins. Performing genomic scaffolding using Hi-C data highly resource-demanding and employs elaborate laboratory steps sample preparation. It starts with building primary sequence assembly as an input, followed computation data, requiring careful validation. article presents technical considerations obtaining optimal results provides test case its to reptile species, Madagascar ground gecko (Paroedura picta). Among metrics are frequently used evaluating results, we investigate validity completeness assessment assemblies single-copy reference orthologues.

Language: Английский

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