Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.
To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
Choulet
Frédéric
F
Institut National de la Recherche Agronomique, Université Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F-63100 Clermont-Ferrand, France. frederic.choulet@clermont.inra.fr
Wicker
Thomas
T
Rustenholz
Camille
C
Paux
Etienne
E
Salse
Jérome
J
Leroy
Philippe
P
Schlub
Stéphane
S
Le Paslier
Marie-Christine
MC
Magdelenat
Ghislaine
G
Gonthier
Catherine
C
Couloux
Arnaud
A
Budak
Hikmet
H
Breen
James
J
Pumphrey
Michael
M
Liu
Sixin
S
Kong
Xiuying
X
Jia
Jizeng
J
Gut
Marta
M
Brunel
Dominique
D
Anderson
James A
JA
Gill
Bikram S
BS
Appels
Rudi
R
Keller
Beat
B
Feuillet
Catherine
C
D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D020451:Contig Mapping; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D017422:Sequence Analysis, DNA; D016615:Telomere / Q000235:genetics; D014908:Triticum / Q000235:genetics*
D004251:DNA Transposable Elements; D018744:DNA, Plant