title: Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome.
abstract: The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps.
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Lindsay A
authors.initials: LA
authors.lastname: Shearer
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Lorinda K
authors.initials: LK
authors.lastname: Anderson
authors.affiliation: Laboratory of Genetics, Wageningen University and Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.affiliation: Laboratory of Bioinformatics, WUR, Droevendaalsesteeg1, 6708 PB Wageningen, The Netherlands.
authors.forename: Sandra
authors.initials: S
authors.lastname: Smit
authors.affiliation: Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.affiliation: Department of Chemistry and Biochemistry, Stephenson Research and Technology Center, University of Oklahoma, Norman, Oklahoma 73019.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.affiliation: Department of Chemistry and Biochemistry, Stephenson Research and Technology Center, University of Oklahoma, Norman, Oklahoma 73019.
authors.forename: Axin
authors.initials: A
authors.lastname: Hua
authors.affiliation: Department of Plant Biology, Cornell University, Ithaca, New York 14853.
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, Colorado 80523 Stephen.Stack@colostate.edu.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Stack
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D018551:Solanum lycopersicum / Q000235:genetics*; D013573:Synaptonemal Complex
chemical_list: D018744:DNA, Plant
keywords: fluorescence in situ hybridization; genome; optical mapping; scaffolds; tomato