Kopecký, D., Martis, M., Číhalíková, J., Hřibová, E., Vrána, J., Bartoš, J., Kopecká, J., Cattonaro, F., Stočes, Š., Novák, P., Neumann, P., Macas, J., Šimková, H., Studer, B., Asp, T., Baird, J.H., Navrátil, P., Karafiátová, M., Kubaláková, M., Šafář, J., Mayer, K., Doležel, J.
PLANT PHYSIOLOGY
163:
1323-1337,
2013
Keywords:
Abstract:
The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence
reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and
has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we
describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity
without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes
and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately
503 coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the
construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced
genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using
GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of
chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization.
They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The
ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying
important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes
enables an overview of chromosome structure and evolution at a resolution never achieved before.
Fulltext: contact IEB authors
IEB authors: Jan Bartoš,
Jarmila Číhalíková,
Jaroslav Doležel,
Miroslava Havránková,
Eva Hřibová,
David Kopecky,
Marie Kubaláková,
Hana Šimková,
Štěpán Stočes,
Jan Vrána
Čeština
English