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Whole-genome landscape of Medicago truncatulasymbiotic genes

Authors :
Pecrix, Yann
Staton, S. Evan
Sallet, Erika
Lelandais-Brière, Christine
Moreau, Sandra
Carrère, Sébastien
Blein, Thomas
Jardinaud, Marie-Françoise
Latrasse, David
Zouine, Mohamed
Zahm, Margot
Kreplak, Jonathan
Mayjonade, Baptiste
Satgé, Carine
Perez, Magali
Cauet, Stéphane
Marande, William
Chantry-Darmon, Céline
Lopez-Roques, Céline
Bouchez, Olivier
Bérard, Aurélie
Debellé, Frédéric
Muños, Stéphane
Bendahmane, Abdelhafid
Bergès, Hélène
Niebel, Andreas
Buitink, Julia
Frugier, Florian
Benhamed, Moussa
Crespi, Martin
Gouzy, Jérôme
Gamas, Pascal
Source :
Nature Plants; December 2018, Vol. 4 Issue: 12 p1017-1025, 9p
Publication Year :
2018

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 truncatulaA17, 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. truncatulagenome 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. truncatulagenome.

Details

Language :
English
ISSN :
2055026X and 20550278
Volume :
4
Issue :
12
Database :
Supplemental Index
Journal :
Nature Plants
Publication Type :
Periodical
Accession number :
ejs47376227
Full Text :
https://doi.org/10.1038/s41477-018-0286-7