High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Сен. 24, 2022

Abstract The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. currently available genomes limit understanding its genetic diversity and discovery valuable alleles breeding. Here, we deeply re-sequence 1,078 silkworms assemble long-read 545 representatives. We construct a high-resolution pan-genome dataset representing almost entire genomic content in silkworm. find that population harbors high density variants identify 7308 new genes, 4260 (22%) core 3,432,266 non-redundant structure variations (SVs). reveal hundreds genes SVs may contribute to artificial selection (domestication breeding) Further, focus on four responsible, respectively, two (silk yield silk fineness) ecologically adaptive traits (egg diapause aposematic coloration). Taken together, our population-scale resources will promote functional genomics studies breeding improvement

Язык: Английский

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High level of novelty under the hood of convergent evolution

Science, Год журнала: 2023, Номер 379(6636), С. 1043 - 1049

Опубликована: Март 10, 2023

Little is known about the extent to which species use homologous regulatory architectures achieve phenotypic convergence. By characterizing chromatin accessibility and gene expression in developing wing tissues, we compared architecture of convergence between a pair mimetic butterfly species. Although handful color pattern genes are be involved their convergence, our data suggest that different mutational paths underlie integration these into development. This supported by large fraction accessible being exclusive each species, including de novo lineage-specific evolution modular optix enhancer. These findings may explained high level developmental drift evolutionary contingency occurs during independent mimicry.

Язык: Английский

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Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 12, 2023

Heliconius butterflies, a speciose genus of Müllerian mimics, represent classic example an adaptive radiation that includes range derived dietary, life history, physiological and neural traits. However, key lineages within the genus, across broader Heliconiini tribe, lack genomic resources, limiting our understanding how neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous assemblies for nine Heliconiini, 29 additional reference-assembled genomes, improve 10 existing assemblies. Altogether, provide dataset annotated genomes total 63 species, including 58 species tribe. We use this extensive to robust dated heliconiine phylogeny, describe major patterns introgression, explore architecture, basis innovations in enigmatic group, assessment putative regulatory regions at stem. Our work illustrates increased resolution provided by such dense sampling improves power test gene-phenotype hypotheses, precisely characterize evolve.

Язык: Английский

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Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence

Genome Research, Год журнала: 2024, Номер unknown

Опубликована: Апрель 8, 2024

Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression reproduction. Despite the need to conserve genome architecture, high level structural variation has been observed species. As species separate diverge, also diverges, becoming increasingly poorly conserved as divergence time increases. However, plant genomes, processes are not well described. Here we use long-read sequencing de novo assembly 33 phylogenetically diverse, wild naturally evolving Eucalyptus species, covering 1–50 million years diverging evolution measure architectural conservation describe divergence. The investigation these genomes revealed following lineage divergence, fragmented by rearrangements. continue accumulation mutations subsequent beyond recognition rearrangements become primary driver loss syntenic regions contribute but at slower pace than We hypothesize duplications translocations potentially greatest contributors

Язык: Английский

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Genome assemblies and other genomic tools for understanding insect adaptation

Current Opinion in Insect Science, Год журнала: 2025, Номер unknown, С. 101334 - 101334

Опубликована: Янв. 1, 2025

Язык: Английский

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Structural Variants and Speciation: Multiple Processes at Play

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 16(3), С. a041446 - a041446

Опубликована: Дек. 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

Язык: Английский

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Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 30, 2024

Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding fragrance hindered by lack a reference genome tea roses. We present first complete telomere-to-telomere (T2T) Rosa gigantea, with high quality (QV > 60), including detailed characterization structural features repetitive regions. The expansion genes associated phenylpropanoid biosynthesis may account unique scent. uncover release rhythm aromatic volatile organic compounds their gene regulatory networks through comparative genomics time-ordered co-expression networks. Analyzes eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights conservation utilization genetic diversity from wild endangered species multi-omics approaches, providing scientific foundation enhancing rose via de novo domestication.

Язык: Английский

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The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Март 11, 2025

Spodoptera frugiperda is a common and severely damaging agricultural pest. In-depth analysis of its population genomics transcriptomics crucial for providing references pest control efforts. This study, focused on the extensive variation in genome size S. frugiperda, constructed pan-genome identified 1.37 Gb non-reference sequences, highlighting significant genetic within population. Analysis Long Terminal Repeat (LTR) Presence/Absence Variation (PAV) suggests that LTR alterations may be one driving factors variation. Additionally, gene PAV revealed variable genes are enriched functions like acetyltransferase activity, which might associated with detoxification, implying diverse selection pressures related to detoxification different populations. Moreover, 19 horizontal transfer (HGT) acquired were reference used this responded 16 treatments. Notably, three HGT-acquired (SFR02618, SFR05248, SFR05249) co-expressed heat shock protein family under treatments Avermectin Cypermethrin. indicate their involvement mechanism coordinated proteins. These results offering new insights into genomic evolution potential genes. A could factor Genes pressure.

Язык: Английский

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Genomic vulnerability of a freshwater salmonid under climate change

Evolutionary Applications, Год журнала: 2023, Номер 17(2)

Опубликована: Окт. 27, 2023

Abstract Understanding the adaptive potential of populations and species is pivotal for minimizing loss biodiversity in this era rapid climate change. Adaptive has been estimated various ways, including based on levels standing genetic variation, presence potentially beneficial alleles, and/or severity environmental Kokanee salmon, non‐migratory ecotype sockeye salmon ( Oncorhynchus nerka ), culturally economically important already impacted by effects To assess its vulnerability moving forward, we integrated analyses genotype‐environment associations, modeling sequence structural genomic variation from 224 whole genomes sampled 22 lakes British Columbia Yukon (Canada). We found that variables extreme temperatures, particularly warmer had most pervasive signature selection genome were strongest predictors putatively both structural. Genomic offset estimates, a measure vulnerability, significantly correlated with higher increases warm further highlighting risk summer heat waves are predicted to increase frequency future. Levels an metric population viability resilience, not offset. Nonetheless, our combined approach highlights importance integrating different sources information data formulate more comprehensive accurate predictions future

Язык: Английский

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Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

Abstract Background Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands gaps, impeding comprehensive understanding genome. Findings Here, we present near-complete gapless for cutting with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem genome, identify 127,681 structural variations (SVs, 0.41 Gb sequence), reflecting divergence leafy lettuce. Interestingly, these SVs are related transposons DNA methylation states. Furthermore, 4,612 whole-genome triplication genes exhibiting expression levels associated low N6-methyladenosine RNA modifications. changes also activation involved callus formation. Conclusions Our assembly, unprecedented achievement establishes solid foundation functional genomics, epigenomics, crop breeding sheds new light on complexity gene regulation dynamics epigenetics evolution.

Язык: Английский

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