Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles. DOI Creative Commons
Gaspar Sánchez-Serna, Jordi Badia‐Ramentol, Paula Bujosa

et al.

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

Published: Aug. 30, 2024

Abstract The impact of gene loss on the divergence taxa and generation evolutionary innovations is a fundamental aspect Evolutionary Biology that remains unclear. Here, using evolution Fibroblast Growth Factors (FGFs) in appendicularians as case study, we investigate how losses have influenced chordates, especially among tunicates. Our work reveals an unprecedented massive all Fgf subfamilies, except for Fgf9/16/20 Fgf11/12/13/14 , which turn suffered two bursts duplications. Phylogenetic inferences genomic analyses synteny conservation, architecture, alternative splicing protein 3D-structure allowed us to reconstruct history appendicularian genes context chordate evolution, providing compelling evidence supporting paracrine secreting functions intracellular respectively. Exhaustive analysis developmental expression Oikopleura dioica model paradigmatic what could be referred “less, but more”, conceptual framework characterized by four associated patterns: conservation ancestral domains; function shuffling between paralogs upon loss; innovation new domains after duplications; extinction linked losses. findings this allow formulate novel hypotheses about potential duplications transition from ascidian-like biphasic lifestyle fully free-living style appendicularians. These include co-option patterning oikoblast responsible house development tail fin; recruitment into mouth, their role modulating neuronal excitability; “anterior tail” FGF signaling mesodermal source retinoic acid signaling; link Fgf7/10/22 Fgf8/17/18 drastic metamorphosis, mesenchymal cells lack absorption appendicularians, contrast ascidians.

Language: Английский

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats DOI Creative Commons
Tristan V. de Jong, Yanchao Pan, Pasi Rastas

et al.

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(4), P. 100527 - 100527

Published: March 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.

Language: Английский

Citations

11
Extreme elevational migration spurred cryptic speciation in giant hummingbirds DOI Creative Commons
Jessie L. Williamson, Ethan F. Gyllenhaal,

Selina M. Bauernfeind

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(21)

Published: May 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.

Language: Английский

Citations

11
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
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
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.

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

Published: March 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.

Language: Английский

Citations

4
Physics and physiology of fish collective movement DOI Creative Commons
Yangfan Zhang, George Lauder

Newton, Journal Year: 2025, Volume and Issue: 1(1), P. 100021 - 100021

Published: March 1, 2025

Language: Английский

Citations

0
Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs DOI Open Access
Sui Liufu,

Qun Lan,

Xiaolin Liu

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(5), P. 1050 - 1050

Published: May 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.

Language: Английский

Citations

10
Unrecognised DNA Degradation in Flash‐Frozen Genetic Samples in Natural History Collections DOI
Alexander T. Salis, Zachary L. Watson, Meghan Forcellati

et al.

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: May 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

Language: Английский

Citations

0
Pseudogenization of NK3 homeobox 2 ( Nkx3.2 ) in monotremes provides insight into unique gastric anatomy and physiology DOI Creative Commons
J.F. Dann, Zhipeng Qu, Linda Shearwin‐Whyatt

et al.

Open Biology, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

The enzymatic breakdown and regulation of food passage through the vertebrate antral stomach pyloric sphincter (antropyloric region) is a trait conserved over 450 million years. Development structures involved underpinned by highly signalling pathway involving hedgehog, bone morphogenetic protein Wingless/Int-1 (Wnt) families. Monotremes are one few lineages where acid-based digestion has been lost, this consistent with lack genes for hydrochloric acid secretion gastric enzymes in genomes platypus ( Ornithorhynchus anatinus ) short-beaked echidna Tachyglossus aculeatus . Furthermore, these species feature unique phenotypes, both truncated aglandular stomachs no pylorus. Here, we explore genetic underpinning monotreme investigating important antropyloric development using newest (mOrnAna1.pri.v4 mTacAcu1) together RNA-seq data. We found that constituents generally conserved, but surprisingly, NK3 homeobox 2 Nkx3.2 was pseudogenized echidna. speculate sequence evolution Grem1 Bmp4 sequences lineage may correlate their pyloric-like restriction convergent loss size genotypes phenotypes teleost be result eco-evolutionary dynamics. These findings reflect effects gene on phenotypic further elucidate control anatomy physiology.

Language: Английский

Citations

2