title: Optical mapping in plant comparative genomics.
abstract: Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants. Direct use of optical mapping to study population-level genetic diversity is currently limited to microbial strain typing and human diversity studies. Nonetheless, optical mapping shows great promise in the study of plant trait development, domestication and polyploid evolution. Here we review the current applications and future prospects of optical mapping in the field of plant comparative genomics.
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian People's Republic of China ; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: J. Craig Venter Institute, Rockville, MD 20850 USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant; D016172:DNA Fingerprinting / Q000379:methods; D018745:Genome, Plant; D010944:Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Comparative genomics; De novo assembly; Optical mapping; Structural variation