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The wheat genome: swimming in an ocean of transposable elements
Frédéric Choulet, Thomas Wicker, Etienne Paux, Cyrille Saintenac, Pierre Sourdille, Beat Keller, Rudi Appels, Catherine Feuillet
To cite this version:
Frédéric Choulet, Thomas Wicker, Etienne Paux, Cyrille Saintenac, Pierre Sourdille, et al.. The wheat genome: swimming in an ocean of transposable elements. ICTE 2008: International Congress on Transposable Elements, Apr 2008, Saint Malo, France. �hal-02820796�
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2008: International Congress on Transposable Elements – Saint Malo, France, April 21-23, 2008
Frédéric CHOULET1, Thomas WICKER2, Etienne PAUX1, Cyrille SAINTENAC1, Pierre SOURDILLE1, Beat KELLER2,
Rudi APPELS3 and Catherine FEUILLET1
1 UMR INRA/UBP 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont-Ferrand, France 2 Institute of Plant Biology, University Zurich, 8008 Zurich, Switzerland
3 Molecular Plant Breeding CRC, State Agriculture Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
With 17 Gb and an hexaploid structure, the bread wheat (Triticum aestivum L.) genome composition and organization is largely unknown and its molecular characterization remains a challenge. Our current knowledge is limited to the analysis of small fragments (150 kb) and random BAC end sequences.
contig size 3.165 Mb predicted genes 50 Sn2 Sr2 Rph7 Stb2 Yr Stagonospora nodorum Puccinia graminis Puccinia hordei Septoria tritici Puccinia striiformis Fhb1 Fusarium graminearum R locus (12 cM) 20 Mb chr 3B 1000 Mb Transposable elements: Gypsy Gypsy Copia Copia LINE LINE CACTA CACTA MITE MITE Unclassified Unclassified Retrotransposons DNA transposons
The
The
wheat
wheat
genome: swimming in an ocean of Transposable Elements
genome: swimming in an ocean of Transposable Elements
•••• Sequencing, annotation and marker development at the Rph7-Fhb1 locus
•••• Establishment of a physical map of the 3B chromosome
The R locus:
A cluster of at least 6 fungal disease resistance loci has been identified on the short arm of chromosome 3B in hexaploid wheat.
15 contigs (~20 Mb in total) are located in this region and 2 contigs spanning disease resistance loci are
currently under sequencing and
annotation.
One of them represents 3,2 Mb and spans the Rph7 and Fhb1 resistance loci.
INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE
INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE
Centre de Clermont
Centre de Clermont--FerrandFerrand--TheixTheix UMR INRA
UMR INRA--UBP 1095, UBP 1095, GGéénnéétiquetique DiversitDiversitéé et et EcophysiologieEcophysiologie des des CCéérrééalesales http://www1.clermont.inra.fr/umr1095/
http://www1.clermont.inra.fr/umr1095/
Using a chromosome-specific approach, we have constructed an integrated physical map of the largest wheat chromosome, 3B (1 Gb), to enhance our knowledge of the structure, function and evolution of the wheat genome.
• 57,000 fingerprinted BACs (8x coverage)
• 1,033 contigs (82% of the chromosome)
• 1,400 molecular markers
• 678 cytogenetically-anchored contigs
chr 3B 1000 Mb
Cytogenetic bins
BAC contigs locus pathogen
TE (and derivatives) 609
- TEs represents 60% of the sequence, the majority of them being
LTR-retrotransposons (72%) and CACTA family DNA transposons (20%). The
curated annotation has lead to detect 609 TEs and truncated derivatives showing variable levels of nested structure.
- The genes and TEs are not randomly distributed along the locus: the length of intergenic regions varies from 500 bps to 283 kb.
LINE MITE unclass. CACTA copia genes gypsy ISBP markers SSR markers c f t 6 0 2 5 c f t 6 0 2 6 c f t 6 0 1 5 c f t 6 0 9 5 c f t 6 0 1 6 c f t 6 0 8 4 c f t 6 0 0 5 c f t 6 0 6 3 c f t 6 0 6 4 c f t 6 0 8 9 c f t 6 0 0 0 c f t 6 0 9 0 c f t 6 0 6 5 c f t 6 0 6 6 c f t 6 0 9 1 c f t 6 0 0 1 c f t 6 0 0 2 c f t 6 0 0 3 c f t 6 0 0 4 c f t 6 0 9 2 c f t 6 0 8 7 c f t 6 0 8 8 c f t 6 0 2 9 c f t 6 0 9 7 c f t 6 0 3 1 c f t 6 0 9 8 c f t 6 0 9 9 c f t 6 1 0 0 c f t 6 1 0 2 c f t 6 0 3 4 c f t 6 1 0 4 c f t 6 0 3 6 c f t 6 1 0 6 c f t 6 1 1 7 c f t 6 0 4 2 c f t 6 0 7 1 c f t 6 0 7 2 c f t 6 0 4 4 c f t 6 0 5 8 c f t 6 0 5 9 c f t 6 0 8 1 c f t 6 0 6 0 c f t 6 0 7 6 c f t 6 0 1 9 c f t 6 0 6 1 c f t 6 0 6 2 c f t 6 0 0 6 c f t 6 0 0 9 c f t 6 0 1 0 c f t 6 0 1 1 c f t 6 0 0 7 c f t 6 0 1 2 c f t 6 0 1 3 c f t 6 0 1 8 Rph7 Fhb1 genes density (/100 kb) 1 0 2 3
This project aims at sequencing and annotating the first Mb-sized contigs available from the hexaploid wheat genome. Preliminary analyses of this 3.2Mb region revealed the presence of 61 different families of repeated elements, of which 15 are represented by more than 10 copies. Furthermore, the 2 major families (Fatima and Sabrina, LTR-retrotransposons) alone represent 84 TE copies and cover 15% of the contig.
In addition, these first large wheat genome sequences are an important resource for new TE discovery. Here, about 30 annotated features are potentially unknown TEs. Deeper analyses now remain to be done to confirm, classify and characterize these new elements. Thus, the sequencing of large contigs provides additional insights, compared to random BAC sequencing, into the genome structure and composition and supports the discovery of new TEs.
The high TE content of the wheat genome can be exploited as an endless source of molecular markers (ISBP: Insertion Site Based Polymorphism). Here, a potential of more than 1200 ISBPs (2 markers per TE) can be designed along the 3.2 Mb.
The data generated by this project provides original and new data on the wheat genome structure, function and evolution at a scale of Mb-sized contigs that has never been studied in wheat so far. In addition, it will allow the cloning of economically important disease resistance genes and QTL and enable the development of perfect markers for marker-assisted selection of these genes.
