دورية أكاديمية
أعرض في EDS

Parallel evolution of amphioxus and vertebrate small-scale gene duplications.

التفاصيل البيبلوغرافية
العنوان: Parallel evolution of amphioxus and vertebrate small-scale gene duplications.
المؤلفون: Brasó-Vives M; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland. marina.brasovives@unil.ch.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland. marina.brasovives@unil.ch., Marlétaz F; Department of Genetics, Evolution and Environment (GEE), University College London, London, UK., Echchiki A; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland., Mantica F; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain., Acemel RD; Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain., Gómez-Skarmeta JL; Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain., Hartasánchez DA; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Le Targa L; IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France.; IHU-Méditerranée Infection, Marseille, France., Pontarotti P; IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France.; IHU-Méditerranée Infection, Marseille, France.; CNRS, Paris, France., Tena JJ; Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain., Maeso I; Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain.; Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain., Escriva H; Biologie Intégrative des Organismes Marins, BIOM, CNRS-Sorbonne University, Banyuls-sur-Mer, France., Irimia M; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.; Pompeu Fabra University (UPF), Barcelona, Spain.; ICREA, Barcelona, Spain., Robinson-Rechavi M; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland. marc.robinson-rechavi@unil.ch.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland. marc.robinson-rechavi@unil.ch.
المصدر: Genome biology [Genome Biol] 2022 Nov 18; Vol. 23 (1), pp. 243. Date of Electronic Publication: 2022 Nov 18.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: London, UK : BioMed Central Ltd
Original Publication: London : Genome Biology Ltd., c2000-
مواضيع طبية MeSH: Lancelets*/genetics, Animals ; Gene Duplication ; Phylogeny ; Vertebrates/genetics ; Vertebrates/metabolism ; Evolution, Molecular
مستخلص: Background: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates.
Results: We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements.
Conclusions: In contrast to their slower molecular and morphological evolution, amphioxus' small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.
(© 2022. The Author(s).)
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معلومات مُعتمدة: 740041 International ERC_ European Research Council
فهرسة مساهمة: Keywords: Amphioxus; Branchiostoma lanceolatum; Comparative genomics; Gene duplication; Genome assembly; Ohnolog; Small-scale duplication; Vertebrate
تواريخ الأحداث: Date Created: 20221119 Date Completed: 20221122 Latest Revision: 20230203
رمز التحديث: 20240829
مُعرف محوري في PubMed: PMC9673378
DOI: 10.1186/s13059-022-02808-6
PMID: 36401278
قاعدة البيانات: MEDLINE
الوصف
تدمد:1474-760X
DOI:10.1186/s13059-022-02808-6