title: Efficient high-throughput sequencing of a laser microdissected chromosome arm.
abstract: BACKGROUND
  Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly.
  
  
  RESULTS
  We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly.
  
  
  CONCLUSIONS
  We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds.
authors.affiliation: Charles University in Prague, Faculty of Science, Prague 2, Czech Republic. eva.seifertova@natur.cuni.cz
authors.forename: Eva
authors.initials: E
authors.lastname: Seifertova
authors.forename: Lyle B
authors.initials: LB
authors.lastname: Zimmerman
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Macha
authors.forename: Svatava
authors.initials: S
authors.lastname: Kubickova
authors.forename: Halina
authors.initials: H
authors.lastname: Cernohorska
authors.forename: Vojtech
authors.initials: V
authors.lastname: Zarsky
authors.forename: Nick D L
authors.initials: ND
authors.lastname: Owens
authors.forename: Abdul K
authors.initials: AK
authors.lastname: Sesay
authors.forename: Tereza
authors.initials: T
authors.lastname: Tlapakova
authors.forename: Vladimir
authors.initials: V
authors.lastname: Krylov
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007834:Lasers; D042282:Microdissection; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA / Q000379:methods*; D014981:Xenopus / Q000235:genetics