First survey of the wheat chromosome 5A composition through a next generation sequencing approach.
Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.
CRIBI Biotechnology Center, University of Padova, Padova, Italy.
Nicola
N
Vitulo
Alessandro
A
Albiero
Claudio
C
Forcato
Davide
D
Campagna
Francesca
F
Dal Pero
Paolo
P
Bagnaresi
Moreno
M
Colaiacovo
Primetta
P
Faccioli
Antonella
A
Lamontanara
Hana
H
Šimková
Marie
M
Kubaláková
Gaetano
G
Perrotta
Paolo
P
Facella
Loredana
L
Lopez
Marco
M
Pietrella
Giulio
G
Gianese
Jaroslav
J
Doležel
Giovanni
G
Giuliano
Luigi
L
Cattivelli
Giorgio
G
Valle
A Michele
AM
Stanca
D032461:Chromosomes, Plant / Q000235:genetics*; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D020451:Contig Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D023061:Gene Order / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques; D017421:Sequence Analysis / Q000379:methods*; D026801:Synteny / Q000235:genetics; D014908:Triticum / Q000235:genetics*
D004251:DNA Transposable Elements; D035683:MicroRNAs