Efficient high-throughput sequencing of a laser microdissected chromosome arm.
Efficient high-throughput sequencing of a laser microdissected chromosome arm.
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DOI：
10.1186/1471-2164-14-357
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发表时间：
2013-05-28
期刊：
影响因子：
4.4
通讯作者：
Krylov V
中科院分区：
文献类型：
--
作者：
Seifertova E;Zimmerman LB;Gilchrist MJ;Macha J;Kubickova S;Cernohorska H;Zarsky V;Owens ND;Sesay AK;Tlapakova T;Krylov V
基因组序列组装是广泛的基因功能和进化研究的关键工具。二倍体两栖动物热带爪蟾（Xenopus tropicalis）由于其实验灵活性、二倍体基因组和早期分支四足动物的分类地位，在3.6亿年前从羊膜动物谱系中分化出来，在这些领域发挥了关键作用。基因组组装和遗传连锁图谱最近已经可用。不幸的是，连锁图谱上的巨大缺口削弱了基因组组装的远程完整性。为了下一代测序和参考基因组的计算定位，我们用激光解剖了热带棘猴7号染色体短臂。这条手臂是特别有趣的，因为它编码性别决定位点，但它的遗传图谱包含很大的缺口，这破坏了可用的基因组组装。对15个激光显微解剖的7p臂进行全基因组扩增，然后进行下一代测序，产生了约3500万个reads，其中超过400万个unique映射到热带棘猴基因组。我们的分析在分析的染色体臂上放置了200多个以前未绘制的支架，为从头基因组组装提供了有价值的低分辨率物理图谱信息。我们提出了一种改进和验证遗传图谱和序列组装的新方法。15个微解剖染色体臂的全基因组扩增为定位先前未定位的支架和基因以及识别错定位支架提供了充足的高质量材料。
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. 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. 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.
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影响因子：
7.2
作者：
Hernandez, Pilar;Martis, Mihaela;Mayer, Klaus F. X.
通讯作者：
Mayer, Klaus F. X.
影响因子：
11.4
作者：
Harland, Richard M.;Grainger, Robert M.
通讯作者：
Grainger, Robert M.
影响因子：
1.7
作者：
Krylov, V.;Tlapakova, T.;Macha, J.
通讯作者：
Macha, J.
DOI：
10.1073/pnas.1016725108
发表时间：
2011-01-04
影响因子：
11.1
作者：
Yang, Hong;Chen, Xi;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
影响因子：
1.5
作者：
Gilchrist, Michael J.
通讯作者：
Gilchrist, Michael J.