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The Repetitive Content in Lupin Genomes

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The Lupin Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

In this chapter, we present the first detailed evaluation of the repetitive compartment in Lupinus genomes. Low-depth next-generation sequencing (NGS) genomic resources from four closely related smooth-seeded Mediterranean lupin species (L. albus, L. angustifolius, L. luteus, and L. micranthus), exhibiting remarkable differences in genome size and chromosome number have been investigated. The repetitive compartment is composed of a wide diversity of repeats and represents 23–51% of the genomes. This compartment is essentially comprised of transposable elements (43–85%), mainly represented by copia and gypsy LTR retrotransposon families. Among the latter, some prominent families (Tekay, Athila, Maximus-SIRE) significantly contribute to genome size differences among species and in shaping different species-specific repeat profiles, regardless of their chromosome numbers. Also particular lineages of these elements have been differentially and recently amplified within species, such as in L. luteus, L. albus, and L. angustifolius. Moreover, this study highlighted the diversity of tandem repeats in lupin genomes, with minisatellites and satellites mostly being species-specific, whereas microsatellites (SSRs) are ubiquitously distributed. Strikingly, L. angustifolius exhibited a tremendous amount of tandem repeats in its genome (26%), including a noteworthy accumulation of one particular hexamer SSR (15.24% of the genome), which demonstrate that also tandem repeats may greatly contribute to genome obesity and dynamics in lupins. Therefore, differential lineage-specific amplifications of retrotransposons and tandem repeats occurred among lupins. Accordingly, this strongly suggests that different processes and mechanisms regulating amplification, proliferation, and clearance of repeats have differentially operated within the same genus among closely related Mediterranean species over the last ~10–12 Myr. Further extension of such evaluation to various representatives of the lupins diversity and outgroups will provide a better overview of the repetitive compartment and its evolutionary dynamics in the genus. Additionally, the genomic resources generated by this work represent a valuable basis to start building a repeats database specifically dedicated to best understand the genomic landscape, repeats distribution, and localization in lupins. This will facilitate further investigations on the functional and evolutionary impact of repeats on genes of interest, such as those responsive for important agronomical, adaptive, and defense features.

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Acknowledgements

We are grateful to INEE-CNRS (France) and to the University of Rennes for their support to this work as part of the research program of the International Associated Laboratory “Ecological Genomics of Polyploidy” involving the University of Rennes (France) and the Iowa State University (Ames, USA). We thank Prof. Barbara Naganowska (Institut of Plant Genetics/PAS, Poznan, Poland) for kindly providing L. angustifolius seeds (IPG2 accession).

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Authors and Affiliations

  1. UMR CNRS 6553 ECOBIO, Université de Rennes 1, 35042, Rennes Cedex, France

    Abdelkader Aïnouche, Aurore Paris, Delphine Giraud, Jean Keller, Pauline Raimondeau, Malika Aïnouche & Armel Salmon

  2. Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, BP42617, 31326, Auzeville, Castanet-Tolosan, France

    Jean Keller

  3. CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), Campus international de Baillarguet, 34398, Montpellier Cedex 5, France

    Frédéric Mahé

  4. Laboratory of Molecular Cytogenetics, Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic

    Pavel Neuman, Petr Novak & Jiri Macas

  5. CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, 34398, Montpellier, France

    Guillaume E. Martin

  6. AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France

    Guillaume E. Martin

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  1. Abdelkader Aïnouche
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Correspondence to Abdelkader Aïnouche .

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  1. Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia

    Karam B. Singh

  2. Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia

    Lars G. Kamphuis

  3. Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia

    Matthew N. Nelson

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Aïnouche, A. et al. (2020). The Repetitive Content in Lupin Genomes. In: Singh, K., Kamphuis, L., Nelson, M. (eds) The Lupin Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-21270-4_12

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