Repeat-based holocentromeres influence genome architecture and karyotype evolution

Cell, Journal Year: 2022, Volume and Issue: 185(17), P. 3153 - 3168.e18

Published: Aug. 1, 2022

The centromere represents a single region in most eukaryotic chromosomes. However, several plant and animal lineages assemble holocentromeres along the entire chromosome length. Here, we compare genome organization evolution as function of type by assembling chromosome-scale holocentric genomes with repeat-based from three beak-sedge (Rhynchospora pubera, R. breviuscula, tenuis) their closest monocentric relative, Juncus effusus. We demonstrate that transition to holocentricity affected 3D architecture redefining genomic compartments, while distributing thousands units genome-wide. uncover complex pubera hides its unexpected octoploidy describe marked reduction number for tenuis, which has only two show fusions, facilitated holocentromeres, promoted karyotype diploidization. Our study thus sheds light on important aspects influenced organization.

Language: Английский

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Chromosome Fissions and Fusions Act as Barriers to Gene Flow betweenBrenthisFritillary Butterflies

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(3)

Published: Feb. 22, 2023

Abstract Chromosome rearrangements are thought to promote reproductive isolation between incipient species. However, it is unclear how often, and under what conditions, fission fusion act as barriers gene flow. Here we investigate speciation two largely sympatric fritillary butterflies, Brenthis daphne ino. We use a composite likelihood approach infer the demographic history of these species from whole-genome sequence data. then compare chromosome-level genome assemblies individuals each identify total nine chromosome fissions fusions. Finally, fit model where effective population sizes migration rate vary across genome, allowing us quantify effects on isolation. show that chromosomes involved in experienced less since onset divergence genomic regions near rearrangement points have further reduction rate. Our results suggest evolution multiple B. ino populations, including alternative fusions same chromosomes, resulted Although unlikely be only processes led this study shows can directly may when karyotypes evolve quickly.

Language: Английский

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The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 15(11), P. a041447 - a041447

Published: Aug. 21, 2023

Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University Neuchâtel, 2000 Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 3Facultad Ciencias Exactas Químicas Naturales, Universidad N3300LQH 4Centre d'Ecologie Fonctionnelle et Evolutive, Université Montpellier, CNRS, EPHE, IRD, 34293 France 5Department Marine Sciences, Gothenburg, 405 30 Sweden 6Centre for Evolutionary 7Department Ecology Cornell University, Ithaca, New York 14853, USA 8Centre Organismal Studies, Heidelberg, 69117 Germany 9Institute Science Technology Austria (ISTA), 3400 Klosterneuburg, 10Faculty Biosciences Aquaculture, Nord 8026 Bodø, Norway 11CIBIO, Centro Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus Vairão, Universidade do Porto, 4485-661 Portugal 12BIOPOLIS Program in Genomics, Biodiversity Land Planning, Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt

Language: Английский

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A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies

Science Advances, Journal Year: 2024, Volume and Issue: 10(16)

Published: April 17, 2024

The impact of large-scale chromosomal rearrangements, such as fusions and fissions, on speciation is a long-standing conundrum. We assessed whether bursts change in chromosome numbers resulting from fusion or fission are related to increased rates Erebia , one the most species-rich karyotypically variable butterfly groups. established genome-based phylogeny used state-dependent birth-death models infer trajectories karyotype evolution. demonstrated that anagenetic changes (i.e., along phylogenetic branches) exceed cladogenetic at events), but, when occur, they mostly associated with fissions rather than fusions. found relative importance differs among clades different ages especially younger, more diverse clades, frequently changes. Overall, our results imply have contrasting macroevolutionary roles rearrangements species diversification.

Language: Английский

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Structural Variants and Speciation: Multiple Processes at Play

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 16(3), P. a041446 - a041446

Published: Dec. 5, 2023

Emma L. Berdan1,2, Thomas G. Aubier3,4, Salvatore Cozzolino5, Rui Faria6,7, Jeffrey Feder8, Mabel D. Giménez9,10, Mathieu Joron11, Jeremy B. Searle12 and Claire Mérot13 1Department of Marine Sciences, Gothenburg University, 40530, Sweden 2Bioinformatics Core, Department Biostatistics, Harvard T.H. Chan School Public Health, Medical School, Boston, Massachusetts 02115, USA 3Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France 4Department Biology, University North Carolina at Chapel Hill, 27599, 5Department Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia 6CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal 7BIOPOLIS Program in Genomics, Biodiversity Land Planning, CIBIO, 4485-661 8Department Biological Notre Dame, Indiana 46556, 9Consejo Nacional Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 10Facultad Ciencias Exactas, Químicas Naturales, Universidad N3300LQH 11Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, CNRS, EPHE, IRD, 12Department Ecology Evolutionary Cornell Ithaca, New York 14853, 13CNRS, 6553 Ecobio, OSUR, Rennes, 35000 Correspondence: claire.merot{at}gmail.com; emma.berdan{at}gmail.com

Language: Английский

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The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction

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

Published: Aug. 5, 2023

Summary The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production, holds tremendous promise sequestration of atmospheric CO 2 . Here, we present chromosomal assemblies, annotations, phylogenomic analysis Lemna genomes that uncover candidate genes responsible metabolic developmental traits family, such as anatomical reduction, adaxial stomata, lack stomatal closure, carbon via crystalline calcium oxalate. have selectively lost required RNA interference, including Argonaute reproductive isolation (the triploid block) haploid gamete formation. Triploid hybrids arise commonly among , found mutations in highly-conserved meiotic crossover could support polyploid meiosis. Syntenic comparisons with Wolffia Spirodela reveal diversification these genera coincided “Azolla event” mid-Eocene, during which aquatic macrophytes reduced high levels to those current ice age. Facile regeneration transgenic fronds from tissue culture, aided by epigenetic silencing, makes a powerful biotechnological platform, exemplified recent engineering high-oil outperforms oil seed crops.

Language: Английский

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Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: July 24, 2023

Holocentric organisms, unlike typical monocentric have kinetochore activity distributed along almost the whole length of chromosome. Because this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for extraordinary rates evolution that many lineages exhibit. Long blocks genome synteny been reported animals with chromosomes despite high rearrangements. Nothing is known from plants, however, fact holocentricity appears played a key role diversification one largest angiosperm genera, Carex (Cyperaceae). In current study, we compared genomes species distantly related Cyperaceae characterize conserved rearranged regions. Our analyses span divergence times ranging between 2 50 million years. We also C. scoparia chromosome-level assembly linkage map same study at population level suppression recombination patterns. found longer than expected under null model random rearrangement breakpoints, even very species. repetitive DNA be non-randomly associated holocentromeres regions genome. The evidence sedges suggests genomic hotspots shape recombination, gene order crossability sedges. This finding help explain why able maintain cohesion face interspecific

Language: Английский

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Chromosome size matters: genome evolution in the cyperid clade

Annals of Botany, Journal Year: 2022, Volume and Issue: 130(7), P. 999 - 1014

Published: Nov. 7, 2022

Abstract Background and Aims While variation in genome size chromosome numbers their consequences are often investigated plants, the biological relevance of remains poorly known. Here, we examine mean cyperid clade (families Cyperaceae, Juncaceae Thurniaceae), which is largest vascular plant lineage with predominantly holocentric chromosomes. Methods We measured 436 species cyperids using flow cytometry, augment these data previously published datasets. then separately compared sizes (2C/2n) amongst major lineages analysed how two genomic traits associated various environmental factors phylogenetically informed methods. Key Results show that have smallest recorded seed a large divergence between values. found smaller chromosomes larger geographical distributions there strong inverse association number across this lineage. Conclusions The distinct patterns might be explained by holokinetic drive. numerous small function to increase genetic diversity where crossovers limited during meiosis.

Language: Английский

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Holocentric repeat landscapes: From micro‐evolutionary patterns to macro‐evolutionary associations with karyotype evolution

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: Aug. 14, 2023

Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain rearrangements lead karyotype changes such as fusions fissions. This is because chromosome segregation during cell division should less affected than in organisms centromere. The relationships between repetitive how they may translate patterns of speciation are though poorly understood. Here, we use reference-free approach based on low-coverage short-read sequencing data characterize the repeat landscape two independently evolved groups: Erebia butterflies Carex sedges. We consider both micro- macro-evolutionary scales investigate differentiation populations association repeats phylogenetic framework Carex. At micro-evolutionary scale, found population increases overall intraspecific genetic among four species. indications an along phylogenies. Altogether, our results suggest associated level clades therefore play role adaptation species diversification.

Language: Английский

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A comparative genomic analysis at the chromosomal-level reveals evolutionary patterns of aphid chromosomes

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 13, 2025

Genomic rearrangements are primary drivers of evolution, promoting biodiversity. Aphids, an agricultural pest with high species diversity, exhibit rapid chromosomal evolution and diverse karyotypes. These variations have been attributed to their unique holocentric chromosomes parthenogenesis, though this hypothesis has faced scrutiny. In study, we generated a chromosomal-level reference genome assembly the celery aphid (Semiaphis heraclei) conducted comparative genomic analysis, revealing varying rates among lineages, positively correlating diversity. Aphid X undergone frequent intra-chromosomal recombination, while autosomes show accelerated inter-chromosomal recombination. Moreover, considering both inter- rearrangements, increased autosomal rearrangement may be common across Aphidomorpha. We identified that expansion DNA transposable elements short interspersed nuclear (SINEs), coupled gene loss duplication associated karyotypic instability (such as RIF1, BRD8, DMC1, TERT), play crucial roles in evolution. Additionally, our analysis revealed mutation detoxification families S. heraclei key factor adapting host plant chemical defenses. Our results provide new insights into evolutionary patterns aphids, aiding understanding diversity adaptive Chromosomal-level comparisons

Language: Английский

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