Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 478652
Title Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome
Author(s) Shearer, L.A.; Anderson, L.K.; Jong, H. de; Smit, S.; Goicoechea, J.L.; Roe, B.A.; Hua, A.; Giovannoni, J.J.; Stack, S.M.
Source G3 : Genes Genomes Genetics 4 (2014)8. - ISSN 2160-1836 - p. 1395 - 1405.
DOI https://doi.org/10.1534/g3.114.011197
Department(s) Laboratory of Genetics
Bioinformatics
EPS
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) extended dna fibers - zea-mays l. - lycopersicon-esculentum - pachytene chromosomes - synaptonemal complexes - 2-dimensional spreads - solanaceous plants - solanum pennellii - multicolor fish - linkage maps
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
Comments
There are no comments yet. You can post the first one!
Post a comment
 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.