title: Advances in plant chromosome genomics.
abstract: Next generation sequencing (NGS) is revolutionizing genomics and is providing novel insights into genome organization, evolution and function. The number of plant genomes targeted for sequencing is rising. For the moment, however, the acquisition of full genome sequences in large genome species remains difficult, largely because the short reads produced by NGS platforms are inadequate to cope with repeat-rich DNA, which forms a large part of these genomes. The problem of sequence redundancy is compounded in polyploids, which dominate the plant kingdom. An approach to overcoming some of these difficulties is to reduce the full nuclear genome to its individual chromosomes using flow-sorting. The DNA acquired in this way has proven to be suitable for many applications, including PCR-based physical mapping, in situ hybridization, forming DNA arrays, the development of DNA markers, the construction of BAC libraries and positional cloning. Coupling chromosome sorting with NGS offers opportunities for the study of genome organization at the single chromosomal level, for comparative analyses between related species and for the validation of whole genome assemblies. Apart from the primary aim of reducing the complexity of the template, taking a chromosome-based approach enables independent teams to work in parallel, each tasked with the analysis of a different chromosome(s). Given that the number of plant species tractable for chromosome sorting is increasing, the likelihood is that chromosome genomics - the marriage of cytology and genomics - will make a significant contribution to the field of plant genetics.
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: dolezel@ueb.cas.cz.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: vrana@ueb.cas.cz.
authors.forename: Jan
authors.initials: J
authors.lastname: Vrána
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: capal@ueb.cas.cz.
authors.forename: Petr
authors.initials: P
authors.lastname: Cápal
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: kubalakova@ueb.cas.cz.
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: buresova@ueb.cas.cz.
authors.forename: Veronika
authors.initials: V
authors.lastname: Burešová
authors.affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic. Electronic address: simkovah@ueb.cas.cz.
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
mesh_terms: D032461:Chromosomes, Plant; D018744:DNA, Plant; D005821:Genetic Techniques; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*
chemical_list: D018744:DNA, Plant
keywords: BAC library; Chromosome sorting; Cytogenetics; DNA arrays; DNA marker development; Flow cytometry; Genome assembly; Mitotic metaphase chromosomes; Next generation sequencing; Physical mapping