Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 10, 2025

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase overcome PCR bias, assemble the 3.1 Gb maned sloth genome, surpassing previous 500 Mb protocol size limit. Our also improves assemblies other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting as valuable sample resources facilitating assembly tiny challenging organisms, our study advances efforts obtain reference genomes all eukaryotes.

Язык: Английский

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A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 18, 2024

Язык: Английский

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A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

Cell Genomics, Год журнала: 2024, Номер 4(4), С. 100527 - 100527

Опубликована: Март 26, 2024

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold increases contiguity 290-fold compared with its predecessor. Gene annotations are now more complete, improving mapping precision genomic, transcriptomic, proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains substrains using mRatBN7.2. defined ∼20.0 million sequence variations, which 18,700 predicted to potentially impact function 6,677 genes. also generated a new genetic map from 1,893 heterogeneous stock rats annotated transcription start sites alternative polyadenylation sites. mRatBN7.2 assembly, along extensive analysis genomic variations among strains, enhances our understanding genome, providing researchers an expanded resource studies involving rats.

Язык: Английский

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Extreme elevational migration spurred cryptic speciation in giant hummingbirds

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(21)

Опубликована: Май 13, 2024

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche may be promoted by local adaptation constrained physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening climatic into varied, seasonal environments. Broader niches can short-lived if diversifying selection and geography promote speciation subdivision across gradients. To illuminate breadth dynamics, we ask how “outlier” defy constraints. Of 363 hummingbird species, giant ( Patagona gigas ) has broadest a large margin. test roles behavior, trade-offs, genetic structure maintaining its exceptional breadth, studied movements, respiratory traits, population genomics. Satellite light-level geolocator tracks revealed an >8,300-km loop migration over Central Andean Plateau. This included 3-wk, ~4,100-m ascent punctuated upward bursts pauses, resembling acclimatization routines human mountain climbers, accompanied surging blood-hemoglobin concentrations. Extreme was deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers gene flow. two forms occur side-by-side differ almost imperceptibly size, plumage, traits. taxon is world’s largest hummingbird, previously undiscovered that describe name here. hummingbirds demonstrate limits on breadth: when ancestral expanded due evolution (or loss) extreme followed.

Язык: Английский

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A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 23, 2023

Abstract The planarian Schmidtea mediterranea can regenerate its entire body from small tissue fragments and is studied as regeneration model species. assembly functional analysis of genomes has proven challenging due high A/T content (70% A/T), repetitive nature, limited transferability routine laboratory protocols to their divergent biochemistry. Only few often fragmented genome assemblies are currently available, open challenges include the provision well-annotated chromosome-scale reference species other planarians for a comparative evolution perspective. Here we report haplotype-phased, high-quality gene annotations sexual S2 strain S. provide putative regulatory region via optimized ATAC-seq ChIP-seq protocols. To additionally leverage sequence conservation element annotations, generated chromatin accessibility data three closest relatives : polychroa , nova lugubris . We find substantial divergence in protein-coding sequences regions, yet reveal remarkable ChIP-mark bearing regions identified promoters enhancers resulting high-confidence set evolutionary conserved provides valuable resource circuits within taxon. In addition, our four first perspective on evolution. Our analyses frequent retrotransposon-associated chromosomal inversions inter-chromosomal translocations that lead degradation synteny across genus. Interestingly, further independent near-complete losses ancestral metazoan two flatworm groups, indicating platyhelminth largely evolve without syntenic constraints. work resources research community sets foundation genomics planarians. contrast between fast structural elements, suggesting unique flatworms where positioning may not be essential.

Язык: Английский

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Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs

Genes, Год журнала: 2023, Номер 14(5), С. 1050 - 1050

Опубликована: Май 8, 2023

The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in determination pork quality. study at mRNA level is particularly crucial for finding molecular approaches to improving meat quality pig breeding. current utilized transcriptome technology explore regulatory mechanisms intramuscular fat (IMF) deposition three core developmental stages (natal stage on day 1, growing 60, finishing 210) Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) common 1 vs. 60 210, GO (Gene Ontology) analysis showed that candidate RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, HOMER1 may be closely related development, while KEGG (Kyoto Encyclopedia Genes Genomes) DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, CPT1B) involved PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway adipocytokine pathway, which might play a pivotal regulation IMF deposition. PPI (Protein-Protein Interaction Networks) found STAT1 gene was top hub gene. Taken together, our provide evidence optimize carcass mass.

Язык: Английский

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Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 7, 2024

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase overcome PCR bias, assembled the 3.1 Gb maned sloth genome, surpassing previous 500 Mb protocol size limit. Our also improves assemblies other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting as valuable sample resources facilitating assembly tiny challenging organisms, our study advances efforts obtain reference genomes all eukaryotes.

Язык: Английский

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Physics and physiology of fish collective movement

Newton, Год журнала: 2025, Номер 1(1), С. 100021 - 100021

Опубликована: Март 1, 2025

Язык: Английский

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Deciphering genetic adaptations of Old World camels through comparative genomic analyses across all camelid species

iScience, Год журнала: 2025, Номер 28(5), С. 112477 - 112477

Опубликована: Апрель 18, 2025

Old World camels exhibit many unique traits for adaptations to desert environments, distinct from New within the same family. Here, we conducted a comparative genomic analysis of three camel species relative four species, as well cattle, pigs, mice, and humans search genes showing positive selection specific variations in camels. We identified under selection, with small indels, inactivated associated lipid metabolism skin characteristics Especially, through experimental validation, confirmed inactivation TAS2R16, gene encoding prominent bitter taste receptor, which could enable consume certain toxic plants other mammals. These findings provide insights into genetic basis underlying distinctive energy metabolism, water-salt homeostasis, dietary

Язык: Английский

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Unrecognised DNA Degradation in Flash‐Frozen Genetic Samples in Natural History Collections

Molecular Ecology Resources, Год журнала: 2025, Номер unknown

Опубликована: Май 5, 2025

ABSTRACT Optimal preservation of tissues from the field to long‐term cryo‐storage is paramount securing genetic resources for research needs. DNA techniques vary, with flash freezing currently considered gold standard in tissue preservation. However, samples presents challenges, necessitating a more comprehensive understanding quantity and quality preserved different archival collections. We compared metrics extractions field‐collected amphibian, squamate bird collections that were flash‐frozen liquid nitrogen or fixed either ethanol lysis buffer prior cryopreservation. also included extracted known tank failures provide baseline degradation under very worst‐case scenario. Flash‐frozen often higher yields DNA, but peak fragment size, percentage fragments larger than 10 kb integrity numbers all significantly reduced first fixative buffers. This pattern was observed across independent between buffer‐preserved pair replicates. Degradation seen distinct failures. suggest occurred during shipping, sample sorting/accession subsequent subsampling when may partially fully thaw, exposing damaging freeze–thaw processes. By contrast, buffers likely protected damage. study highlights using multiple methods minimising cycles most robust protection against sources encountered by

Язык: Английский

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