Annelid Comparative Genomics and the Evolution of Massive Lineage-specific Genome Rearrangement in Bilaterians

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 13, 2024

Abstract The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained others. However, the evolutionary forces driving these differences by which they emerge have remained largely uncharacterized. Here, we analyze across phylum Annelida using 23 chromosome-level annelid genomes. We find while many lineages maintained bilaterian structure, Clitellata, group containing leeches earthworms, possesses completely scrambled develop rearrangement index to quantify extent evolution show that, compared bilaterians, earthworms among most rearranged any currently sampled species. further can be classified two distinct categories—high low rearrangement—largely influenced presence or absence, respectively, chromosome fission events. Our findings demonstrate animal variable within reveal occur both gradual, stepwise fashion, rapid, all-encompassing changes over short timescales.

Language: Английский

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Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Genome Research, Journal Year: 2025, Volume and Issue: 35(1), P. 78 - 92

Published: Jan. 1, 2025

Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis suggesting macrosynteny be potentially powerful source phylogenetic information. Finally, show that rearrangements dispersion from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum, reveal group fission can occur very frequently specific lineages.

Language: Английский

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Evidence for multiple independent expansions of Fox gene families within flatworms

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

Abstract Expansion and losses of gene families are important drivers molecular evolution. A recent survey Fox genes in flatworms revealed that this superfamily multifunctional transcription factors, present all animals, underwent extensive expansions during platyhelminth In paper, I analyzed complement four additional species platyhelminths, represent early-branching lineages the flatworm phylogeny: catenulids ( Stenostomum brevipharyngium leucops ) macrostomorphs Macrostomum hystrix cliftonense ). Phylogenetic analysis from expanded set provided evidence for multiple independent within flatworms. Notably, FoxG , a panbilaterian brain-patterning gene, appears to be least susceptible duplication, while FoxJ1 conserved ciliogenesis factor, has undergone expansion various lineages. Analysis single-cell atlas S. combined with RNA situ hybridization, elucidated tissue-specific expression selected genes: is expressed brain, three FoxN2/3-2, FoxO4 FoxP1 pharyngeal cells likely glandular function, one FoxQD paralogs specifically protonephridium. Overall, evolution characterized by an early contraction complement, followed lineage-specific have enabled co-option newly evolved into novel physiological developmental functions. Statements Declarations The author no competing interests declare relevant content article. research was funded Alexander von Humboldt Foundation (The Research Fellowship Postdoctoral Researchers) Polish National Agency Academic Exchange (Polish Returns NAWA grant no. BPN/PPO/2023/1/00002).

Language: Английский

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Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms

Journal of Molecular Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 18, 2025

Language: Английский

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Chromatin remodeling protein BPTF mediates chromatin accessibility at gene promoters in planarian stem cells

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

Published: March 11, 2025

The regulation of chromatin accessibility is essential in eukaryotic cells as one several mechanisms that ensure gene activation occurs at appropriate times and cell types. Accordingly, mutations remodeling proteins are linked to many different developmental disorders cancers. One example a protein has been both abnormalities cancer BPTF/NURF301, the largest subunit Nucleosome Remodeling Factor (NuRF) complex. BPTF not only important for formation NuRF but also helps direct its activity particular regions by preferentially binding histone H3 lysine four trimethylation (H3K4me3). Notably, defects caused knockdown bptf Xenopus embryos mimic those wdr5, core all H3K4me3 methyltransferase complexes. However, mechanistic details how where BPTF/NuRF recruited regulate expression vary between studies have largely tested vitro and/or cultured cells. Improving our understanding this complex targets specific loci regulates their an organismal context will provide insight into pathogenic disrupt normal, vivo, cellular functions. Here, we report findings on role maintaining function planarian (Schmidtea mediterranea) stem We find depletion primarily affects promoters near transcription start sites (TSSs). BPTF-dependent loss did correlate with decreased when considered affected loci. found genes marked Set1-dependent H3K4me3, MLL1/2-dependent showed increased sensitivity accessibility. In addition, (Smed-bptf) produces loss-of-function phenotypes similar Smed-set1. S.mediterranea homolog (SMED-BPTF) normal homeostasis tissues, potentially through subset By identifying lose after BPTF, identified cohort may functions biology.

Language: Английский

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An integrative taxonomic approach reveals unexplored diversity in Croatian planarians

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

Abstract Background Freshwater ecosystems are among the most endangered habitats on Earth, with approximately one-fourth of aquatic species at risk extinction. Effective conservation efforts require comprehensive monitoring and accurate identification, including often overlooked groups. DNA barcoding promises rapid accessible identification but requires availability “universal” primer pairs robust, taxonomically curated reference libraries. Planarian flatworms one such group for which these resources currently lacking, even though they common constituents freshwater worldwide. As a result, true extent planarian diversity remains underappreciated in many areas. Results Motivated by highly skewed representation current GenBank records gene mitochondrial cytochrome c oxidase subunit I (COI), we optimised existing primers tested them planarians collected species-rich but, so far, poorly surveyed region Croatia. Using an integrative approach combining new primers, traditional taxonomy karyology, generated COI barcode sequences European dugesiids, dendrocoelids planariids, which, case latter two groups, represent substantial increase number entries those families. Our resulted several significant findings, description pigmented Dendrocoelum species, pigmentatum sp. nov, discovery differentiated haplotypic clades Schmidtea lugubris , rediscovery Polycladodes alba Croatia after century. Conclusions Overall, our work extends utility species-level to previously inaccessible Additionally, it integrates as underexplored into endeavour systematically describe fauna Europe. The expansion known Croatian from eight sixteen new, large continental Europe, demonstrate effectiveness approach. highlights planarians, Europe supports practical preserve biodiversity.

Language: Английский

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A comprehensive pipeline for genome annotation across species: a case study onSchmidtea mediterranea

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 20, 2025

Abstract Background Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as Schmidtea mediterranea . Findings To address these challenges, we developed a flexible and scalable pipeline that integrates short-read (Illumina) long-read (PacBio) sequencing technologies. The combines reference-based de novo assembly methods, effectively handling variability alternative splicing events. Functional is conducted to filter out low-confidence transcripts ensure biological relevance. Applying this the asexual strain of S. revealed thousands previously undescribed putative genes transcripts, improved existing gene models, highlighting its utility annotating complex, underexplored genomes. Conclusions modularity comprehensiveness our adaptability across diverse species, making it valuable tool genomes non-model supporting broader research. source code implementation details are available at https://github.com/Norreanea/SmedAnno

Language: Английский

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A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals

Cell Reports, Journal Year: 2024, Volume and Issue: 43(10), P. 114777 - 114777

Published: Sept. 19, 2024

Language: Английский

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Allometry of cell types in planarians by single-cell transcriptomics

Science Advances, Journal Year: 2025, Volume and Issue: 11(19)

Published: May 7, 2025

Allometry explores the relationship between an organism’s body size and its various components, offering insights into ecology, physiology, metabolism, disease. The cell is basic unit of biological systems, yet study cell-type allometry remains relatively unexplored. Single-cell RNA sequencing (scRNA-seq) provides a promising tool for investigating allometry. Planarians, capable growing degrowing following allometric scaling rules, serve as excellent model these studies. We used scRNA-seq to examine in asexual planarians different sizes, revealing that they consist same types but varying proportions. Notably, gut basal cells are most responsive changes size, suggesting role energy storage. capture regulated gene modules distinct response size. This research sheds light on molecular cellular aspects underscores utility investigations.

Language: Английский

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RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts

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

Published: July 21, 2024

The overwhelming majority of RNA species isolated from cells or tissues using organic extraction are ribosomal RNAs (rRNA), whereas a relatively small percentage messenger (mRNA). For studies that seek to detect mRNA transcripts and measure changes in their expression, this lopsided ratio desired undesired creates significant challenge obtaining sensitive reproducible results. One method for improving detection is selectively amplify polyadenylated (polyA) molecules when generating RNA-seq libraries, strategy generally very successful many species. However, less effective starting with total some e.g., the planarian

Language: Английский

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