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eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA

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Molecular Biology and Evolution @molbioevol.bsky.social · 1d

Congratulations, Zheng and colleagues, thank you for publishing your research with MBE!

Reposted by Molecular Biology and Evolution

赵征 Zheng ZHAO @zhaozheng0503.bsky.social · 1d

1/5: ☺️☺️ Recently, we have published a database paper in the MBE journal @molbioevol.bsky.social titled "eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA". #eccDNA #disease #multi_species

academic.oup.com/mbe/article/...

Abstract. Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across

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Molecular Biology and Evolution @molbioevol.bsky.social · 1d

Fantastic paper Claudèle, thank you for publishing with MBE!

From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance

Reposted by Molecular Biology and Evolution

Claudèle Lemay-St-Denis @claudele.bsky.social · 2d

How does catalysis emerge from non-catalytic domains?

In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.

A striking case of catalysis evolving from binding.

Molecular Biology and Evolution @molbioevol.bsky.social · 7d

@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity.

🔗 doi.org/10.1093/molbev/msaf215

#evobio #molbio

Abstract. How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were disco

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Molecular Biology and Evolution @molbioevol.bsky.social · 4d

Lin et al. present a chromosome-level genome of Eden's whale to elucidate the speciation and taxonomy of balaenopterids; findings show Eden's whale is the sister species of Bryde's whale, sharing a common ancestor approximately 7.84 Mya.

🔗 doi.org/10.1093/molbev/msaf234

#evobio #molbio #whale

MBE | Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex

Seasonal Influenza Viruses Show Distinct Adaptive Dynamics During Growth in Chicken Eggs

Molecular Biology and Evolution @molbioevol.bsky.social · 4d

Kistler & Bedford analysed the evolution of human influenza virus from strains grown in chicken eggs for several generations for vaccine production.

🔗 doi.org/10.1093/molbev/msaf227

#evobio #molbio #virus #influenza

Abstract. Human influenza viruses are grown in chicken eggs for vaccine production. Sequences of these egg-passaged viruses give us the opportunity to exam

Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance

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Molecular Biology and Evolution @molbioevol.bsky.social · 4d

Goya & Greninger sequenced human parainfluenza virus genomes, with their findings highlighting distinct evolutionary histories of HPIV-2 and HPIV-4, raising hypotheses around complex Paramyxoviridae zoonotic events.

🔗 doi.org/10.1093/molbev/msaf217

#evobio #molbio #virus

Abstract. Human parainfluenza virus 2 (HPIV-2) and human parainfluenza virus 4 (HPIV-4) are significant but underappreciated respiratory pathogens, particu

Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota

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Reposted by Molecular Biology and Evolution

Dominik Melville @ecoevodom.bsky.social · 4d

The extent to which closely related hosts share similar gut microbiota fascinates me. Work that truely stands out to me comes from @bperezlamarque.bsky.social and colleagues using process-based modelling over correlative approaches - a 'must' read #mevosky academic.oup.com/mbe/article/...

Abstract. How host-associated microbial communities evolve as their hosts diversify remains equivocal: how conserved is their composition? What was the com

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies

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Molecular Biology and Evolution @molbioevol.bsky.social · 4d

Congratulations on this excellent article, Anastasia and team!

Reposted by Molecular Biology and Evolution

Ana Ignatieva @anaignatieva.bsky.social · 7d

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla

From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance

4 37 61

Molecular Biology and Evolution @molbioevol.bsky.social · 7d

@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity.

🔗 doi.org/10.1093/molbev/msaf215

#evobio #molbio

Abstract. How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were disco

eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA

Reposted by Molecular Biology and Evolution

Javier Santoyo @jsantoyo.bsky.social · 7d

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information. #Ychromosome #EvolutionaryInformation #GeneticVariants #HumanGenome @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/article/...

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Molecular Biology and Evolution @molbioevol.bsky.social · 8d

Zhang et al. eccDNABase, a comprehensive and curated resource for browsing, searching, and analyzing Extrachromosomal circular DNAs across multiple species.

🔗 doi.org/10.1093/molbev/msaf223

#evobio #molbio #compbio

Abstract. Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information

Molecular Biology and Evolution @molbioevol.bsky.social · 8d

Köksal et al. introduce the Y-chromosomal ancestral-like reference sequence to improve the detection of evolutionarily informative variants on the Y chromosome, and introduce the tool polaryzer to annotate variants in Y chromosome data

🔗 doi.org/10.1093/molbev/msaf222

#evobio #molbio

Abstract. Reference sequences are essential for reproducible genetic analyses but are often chosen without regard to evolutionary relevance within the anal

Flexibility in Gene Coexpression at Developmental and Evolutionary Timescales

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Molecular Biology and Evolution @molbioevol.bsky.social · 8d

Fischer et al. characterize differences in gene network connectivity and density, suggesting that flexibility in gene coexpression relationships could promote evolvability.

🔗 doi.org/10.1093/molbev/msaf194

#evobio #molbio

Abstract. The explosion of next-generation sequencing technologies has allowed researchers to move from studying single genes to studying thousands of gene

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors

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Molecular Biology and Evolution @molbioevol.bsky.social · 8d

Pang, Liu & Zhang combined theoretical analyses and simulations to evaluate the robustness of methods to detect gene flow in the face of rate variation across phylogenetic timescales.

🔗 doi.org/10.1093/molbev/msaf216

#evobio #molbio

Abstract. Recent theoretical and algorithmic advances in introgression detection, coupled with the growing availability of genome-scale data, have highligh

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Molecular Biology and Evolution @molbioevol.bsky.social · 8d

Great work, Sven and colleagues. Thank you for publishing your research with MBE!

Resolving the stasis-dynamism paradox: Genome evolution in tree ferns

Reposted by Molecular Biology and Evolution

PM Delaux @pierremarcdelaux.bsky.social · 8d

...and three more fern genomes @molbioevol.bsky.social !

Not-so-static static lineages!

academic.oup.com/mbe/advance-...

Abstract. The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental

Evolutionary refinement of mitochondrial and plastid targeting sequences coincides with the late diversification of land plants

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Reposted by Molecular Biology and Evolution

Sven Gould @turbokraken.bsky.social · 15d

The evolution of land plants involved a charge-based adaption in the targeting sequences for #mitochondria and #chloroplasts and the origin of their de/phosphorylation.

#science 🧪

academic.oup.com/mbe/advance-...

Abstract. Plastids and mitochondria are key to plant survival and adaptation. The evolutionary progress of land plants (embryophytes) witnessed gene and ge