Abstract

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.

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Data availability

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PSQE00000000. The version described in this paper is version PSQE01000000. Raw reads from PacBio, ChIP-seq and small RNAseq experiments have been deposited at the Sequence Read Archive (SRA) (project accession number: SRP131849). Data related to gene annotation, transposable element annotation and ChIP-seq analyses, as well as Supplementary Table 6, are available at the web portal: https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/; downloads section.

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Acknowledgements

We thank C. Ben and L. Gentzbittel (EcoLab, Université de Toulouse, CNRS, Toulouse INP, UPS, France), G. Aubert, R. Thompson and K. Gallardo (INRA, UMR 1347, Agroécologie, Dijon, France) and B. Gronenborn (I2BC, CNRS, Paris Sud, CEA, University of Paris Saclay, Gif sur Yvette, France) for providing small RNA data on disease responses, seeds and viroid-infected plants, respectively, as well as N. Peeters (LIPM, Toulouse) for mRNA data used for genome annotation. We thank M.C. Le Paslier for her help in Illumina sequencing. This work was supported by the ANR grants EPISYM (grant no. ANR-15-CE20-0002), NODCCAAT (no. ANR-15-CE20-0012), REGULEG (no. ANR-15-CE20-0001), the ‘Laboratoire d’Excellence (LABEX)’ TULIP (no. ANR-10-LABX-41), the LABEX Saclay Plant Sciences (SPS; no. ANR-10-LABX-40) and the European Research Council (no. ERC-SEXYPARTH), and we made use of data previously generated in the ANR SYMbiMICS (ANR-08-GENO-106) and the INRA SPE EPINOD projects. The sequencing platform was supported by France Génomique National infrastructure (grant no. ANR-10-INBS-09) and by the GET-PACBIO programme (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020). We are grateful to the Genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul) for providing computing and storage resources. C. Satgé was supported by a doctoral grant from the French Ministry of Education and Research.

Author information

Author notes

    • Carine Satgé

    Present address: CNRGV, INRA, Castanet-Tolosan, France

  1. These authors contributed equally: Y. Pecrix, S. Evan Staton, E. Sallet, C. Lelandais-Brière.

  2. These authors jointly supervised this work: J. Gouzy, M. Crespi, P. Gamas.

Affiliations

  1. LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France

    • Yann Pecrix
    • , Erika Sallet
    • , Sandra Moreau
    • , Sébastien Carrère
    • , Baptiste Mayjonade
    • , Carine Satgé
    • , Frédéric Debellé
    • , Stéphane Muños
    • , Andreas Niebel
    • , Jérôme Gouzy
    •  & Pascal Gamas
  2. University of British Columbia, Vancouver, Canada

    • S. Evan Staton
  3. IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France

    • Christine Lelandais-Brière
    • , Thomas Blein
    • , David Latrasse
    • , Magali Perez
    • , Abdelhafid Bendahmane
    • , Florian Frugier
    • , Moussa Benhamed
    •  & Martin Crespi
  4. IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France

    • Christine Lelandais-Brière
    • , Thomas Blein
    • , David Latrasse
    • , Magali Perez
    • , Abdelhafid Bendahmane
    • , Florian Frugier
    • , Moussa Benhamed
    •  & Martin Crespi
  5. LIPM, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France

    • Marie-Françoise Jardinaud
  6. GBF, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France

    • Mohamed Zouine
    •  & Margot Zahm
  7. AGROECOLOGIE, INRA, Dijon, France

    • Jonathan Kreplak
  8. CNRGV, INRA, Castanet-Tolosan, France

    • Stéphane Cauet
    • , William Marande
    • , Céline Chantry-Darmon
    •  & Hélène Bergès
  9. INRA, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France

    • Céline Lopez-Roques
    •  & Olivier Bouchez
  10. INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France

    • Aurélie Bérard
  11. IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France

    • Julia Buitink

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Contributions

S.Mo., B.M., C.L-R. and O.B. prepared DNA samples and performed PacBio sequencing. S.Cau., C.C-D., W.M. and H.B. built the Bionano optical maps. B.M., J.G., W.M., S.Mu. and A.Ber. designed and performed Illumina seq of BAC end sequencing (EcoR1 library). F.D. prepared DNA samples and managed Illumina sequencing. J.G. assembled the genome. E.S., S.Car. and J.G. annotated protein-coding genes and miRNAs. S.E.S. annotated and analysed repeats and transposable elements. S.Car. developed the Medicago bioinformatics portal. J.K. positioned HapMap data on the new reference genome. C.S. and C.L.-B. prepared samples for the sRNA analyses. C.L.-B. conducted the miRNA analyses. T.B., C.L.-B. and Y.P. conducted the siRNA analyses. S.Mo. and M.P. prepared the histone mark samples. D.L. and M.P. performed the ChIP experiments. M.B., D.L. and A.Ben. performed ChIP-seq. M.Za., M.Zo., M.B., S.Car., Y.P. and P.G. performed the analysis of the ChIP-seq data. Y.P. and P.G. conducted the lncRNA analyses. Y.P., S.Car. and P.G. performed the gene family analyses. J.G. and T.B. performed the sRNA and mRNA expression analyses. M.-F.J. performed the gene and siRNA differential expression analyses. Y.P. and P.G. performed the integrated analyses of the symbiotic islands. P.G., J.G., M.C., A.N. and J.B. contributed to the project set-up. P.G., J.G., S.E.S. and C.L.-B. wrote the manuscript, with contributions from M.C., F.F., J.B., B.M., Y.P., F.D., A.N., M.Zo., E.S. and S.Mu. P.G., J.G. and M.C. coordinated the project.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Jérôme Gouzy or Pascal Gamas.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–6, Supplementary Tables 1 and 2, Supplementary Notes on genome sequencing and assembly; genome annotation; transposable elements and repeats; transcriptome analysis; analysis of symbiosis-related islands, and Supplementary References. Supplementary Table 6 (M. truncatula gene annotation, RNAseq data, MtV4 ID and affymetrix probe correspondence) can be found at https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/; downloads section.

  2. Reporting Summary

  3. Supplementary Table 3

    Transduplicate analyses

  4. Supplementary Table 4

    miRNA analyses

  5. Supplementary Table 5

    siRNA analyses

  6. Supplemental Table 7

    Expression correlation analyses

  7. Supplementary Table 8

    Genes expressed in symbiosis-related islands

  8. Supplementary Table 9

    Conservation of symbiosis-related island genes in M. truncatula R108 genome

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DOI

https://doi.org/10.1038/s41477-018-0286-7