De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar DOI Creative Commons
Lindsey Hauff,

Noa Elosmie Rasoanaivo,

Andriamahery Razafindrakoto

et al.

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

Evolution of a novel adrenal cell type that promotes parental care DOI
Natalie Niepoth, Jennifer R. Merritt, M Umiński

et al.

Nature, Journal Year: 2024, Volume and Issue: 629(8014), P. 1082 - 1090

Published: May 15, 2024

Language: Английский

Citations

9
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence DOI Creative Commons
Mario Ivanković, Jeremias N. Brand, Luca Pandolfini

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 18, 2024

Language: Английский

Citations

9
Long-read sequencing and genome assembly of natural history collection samples and challenging specimens DOI Creative Commons

Bernhard Bein,

Ioannis Chrysostomakis, Larissa Souza Arantes

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 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.

Language: Английский

Citations

1
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine DOI Creative Commons
Sinan U. Umu, Vanessa Molin Paynter,

Håvard Trondsen

et al.

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100348 - 100348

Published: June 25, 2023

The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct where small RNA sequencing is hard achieve. further describe score expected that can be used assess completeness assemblies. closes long-persisting field by facilitating automated pipelines deeper studies into evolution regulation, even organisms.

Language: Английский

Citations

18
Genome annotation: From human genetics to biodiversity genomics DOI Creative Commons
Roderic Guigó

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100375 - 100375

Published: Aug. 1, 2023

Within the next decade, genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand biology species. This challenging due transcriptional complexity genomes, which encode hundreds thousands transcripts multiple types. Among these, a small set protein-coding mRNAs play disproportionately large role defining phenotypes. Due their sequence conservation, orthology can established, making it possible define universal catalog genes. should substantially contribute uncovering genomic events underlying emergence piece briefly reviews basics gene prediction, discusses challenges finalizing annotation human genome, and proposes strategies for producing annotations across Tree Life. lays groundwork obtaining all genes-the Earth's code life.

Language: Английский

Citations

17
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography DOI Creative Commons
Yury V. Bukhman, Phillip A. Morin,

Susanne Meyer

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 20, 2024

Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance cancer. To further this other whale-related research, we report a reference-quality, long-read-based genome assembly of fascinating species. We assembled from PacBio long reads utilized Illumina/10×, optical maps, Hi-C data for scaffolding, polishing, manual curation. also provided read RNA-seq facilitate annotation by NCBI Ensembl. Additionally, annotated both haplotypes using TOGA measured size flow cytometry. then compared whale with cetaceans artiodactyls, including vaquita (Phocoena sinus), world's smallest cetacean, investigate whale's unique biological traits. found dramatic amplification several genes resulting recent burst segmental duplications, though possible connection between giant body requires study. discovered sites insulin-like growth factor-1 gene correlated cetaceans. Finally, our examine heterozygosity historical demography Pacific Atlantic populations, that genomes populations are highly heterozygous their genetic isolation dates last interglacial period. Taken together, these results indicate how high-quality, will serve as resource biology, evolution, conservation research.

Language: Английский

Citations

8
Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo DOI Creative Commons
Marlies E. Oomen, Maria‐Elena Torres‐Padilla

EMBO Reports, Journal Year: 2024, Volume and Issue: 25(4), P. 1721 - 1733

Published: March 25, 2024

Abstract Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish and acting a source genome instability, several these have been co-opted part complex system regulation. Many TEs lost transposition ability their transcriptional potential has tampered result interactions with the host evolutionary time. It proposed that ultimately repurposed to function gene regulatory hubs scattered genomes. In early in particular, find perfect environment naïve chromatin escape repression by host. As consequence, it is thought hosts found ways co-opt TE sequences regulate large-scale changes transcription state this review, we discuss examples during development, for co-option regulation pressures on

Language: Английский

Citations

7
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas DOI Creative Commons
Wei E. Gordon, Seungbyn Baek, Hai P. Nguyen

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 9, 2024

Abstract Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq scATAC-seq) on insectivorous ( Eptesicus fuscus ; big brown bat) frugivorous Artibeus jamaicensis Jamaican fruit bat kidneys pancreases identify key cell population, gene expression regulatory differences associated with that also relate to human disease, particularly diabetes. We find a decrease loop of Henle an increase collecting duct cells, differentially active genes elements involved fluid electrolyte balance kidney. The pancreas shows endocrine exocrine insulin regulation. these bats share several characteristics Combined, our work provides insights from mammal could be leveraged for therapeutic purposes.

Language: Английский

Citations

6
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence DOI Creative Commons
Mario Ivanković, Jeremias N. Brand, Luca Pandolfini

et al.

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

Published: Dec. 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.

Language: Английский

Citations

12
Orthology inference at scale with FastOMA DOI Creative Commons
Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi

et al.

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

Published: Jan. 31, 2024

Abstract The surge in genome data, with ongoing efforts aiming to sequence 1.5M eukaryotes a decade, could revolutionise genomics, revealing the origins, evolution, and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly such large datasets. Addressing this, “FastOMA” provides linear scalability, enabling processing thousands eukaryotic genomes within day. FastOMA maintains high accuracy resolution well-established OMA approach benchmarks. is available at https://github.com/DessimozLab/FastOMA/ .

Language: Английский

Citations

4