Luo, M.-Ch., Ma, Y., You, F. M., Anderson, O. D., Kopecký, D., Šimková, H., Šafář, J., Doležel, J., Gill, B., McGuire, P., Dvořák, J.
BMC GENOMICS
11:
122,
2010
Klíčová slova:
Abstrakt:
Background: The presence of closely related genomes in polyploid species makes the assembly of total genomic
sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not
impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach
employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC
contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-informationcontent-
fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is
possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous
restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical
mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility
of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is
possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted
chromosomes and bypass the obstacles created by polyploidy.
Results: The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global
BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library
composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and
complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to
estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a
single chromosome arm. A large portion of the remaining clones was shown to be library contamination from
other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.
Conclusions: The negligibly low level of incorporation of clones from homoeologous chromosome arms into a
contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global
BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to
that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome
sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for
polyploid species containing smaller, more gene-rich genomes.
Fulltext: kontaktujte autory z ÚEB
Autoři z ÚEB: Jaroslav Doležel,
David Kopecky,
Jan Šafář,
Hana Šimková
Čeština
English