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Statements

Subject Item
n2:RIV%2F00027162%3A_____%2F13%3A%230001029%21RIV14-MZE-00027162
rdf:type
skos:Concept n15:Vysledek
dcterms:description
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 similar to 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. 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 similar to 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. 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. 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 similar to 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. 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 similar to 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. 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.
dcterms:title
Efficient high-throughput sequencing of a laser microdissected chromosome arm Efficient high-throughput sequencing of a laser microdissected chromosome arm
skos:prefLabel
Efficient high-throughput sequencing of a laser microdissected chromosome arm Efficient high-throughput sequencing of a laser microdissected chromosome arm
skos:notation
RIV/00027162:_____/13:#0001029!RIV14-MZE-00027162
n15:predkladatel
n16:ico%3A00027162
n3:aktivita
n5:I n5:S n5:P n5:Z
n3:aktivity
I, P(GPP502/11/P522), S, Z(MSM0021620858), Z(MZE0002716202)
n3:cisloPeriodika
357
n3:dodaniDat
n12:2014
n3:domaciTvurceVysledku
n9:4702077 n9:8408033
n3:druhVysledku
n20:J
n3:duvernostUdaju
n18:S
n3:entitaPredkladatele
n17:predkladatel
n3:idSjednocenehoVysledku
72069
n3:idVysledku
RIV/00027162:_____/13:#0001029
n3:jazykVysledku
n11:eng
n3:klicovaSlova
Xenopus; Tropicalis; Chromosomes; Next generation sequencing; WGA; Genetic map
n3:klicoveSlovo
n8:Xenopus n8:Chromosomes n8:WGA n8:Genetic%20map n8:Tropicalis n8:Next%20generation%20sequencing
n3:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n3:kontrolniKodProRIV
[B379B25B2F32]
n3:nazevZdroje
BMC Genomics
n3:obor
n19:EB
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
11
n3:projekt
n10:GPP502%2F11%2FP522
n3:rokUplatneniVysledku
n12:2013
n3:svazekPeriodika
14
n3:tvurceVysledku
Gilchrist, M. J. Zimmerman, L. B. Krylov, V. Černohorská, Halina Owens, N. D. L. Zarsky, V. Seifertova, E. Macha, J. Sesay, A. Kubíčková, Svatava Tlapakova, T.
n3:wos
000321385600001
n3:zamer
n4:MZE0002716202 n4:MSM0021620858
s:issn
1471-2164
s:numberOfPages
9
n14:doi
10.1186/1471-2164-14-357