Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.
Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.
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DOI：
10.1093/gbe/evr038
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发表时间：
2011
影响因子：
3.3
通讯作者：
Dijkwel PP
中科院分区：
文献类型：
--
作者：
Lai AG;Denton-Giles M;Mueller-Roeber B;Schippers JH;Dijkwel PP
亲缘关系密切的个体的基因组测序已经产生了将基因组进化与表型变异联系起来的有价值的见解。然而，测序技术的进步也导致了基于参考基因组组装的质量较差的基因组数量的增加，这些参考基因组可能具有高度分化或单倍型区域。拟南芥的自交特性对测序项目具有优势，因为它的基因组大多是纯合的。为了确定拟南芥起草的基因组在保守程度较低的区域的准确性，我们对Landsberg erecta(LER-0)加入的∼371kb基因组区间进行了重新测序实验。我们使用远程聚合酶链式反应方法识别了LER-0和参考登录号COL-0之间的新结构变异(SVS)，以生成具有位置信息的Illumina数据集，即具有映射到已知位置的读数的数据集。位置信息对于精确的基因组组装和SVS的分辨率非常重要，特别是在高度重复或重复的区域。从LER-0草案中鉴定出61个具有错误组装签名的区域，这表明存在草案序列中没有表现的新的SVS。其中60个是通过使用我们的数据集的迭代映射来解决的。从这项研究中发现了15个大的indels(>；100bp)，它们要么位于蛋白质编码区，要么位于上游调控区，这表明在LER-0中形成了新的等位基因或改变了现有基因的调控。我们建议未来的基因组测序实验遵循一种基于克隆的方法，该方法结合位置信息，最终揭示不同材料之间的单倍型特定差异。
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a ∼371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.
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影响因子：
3.7
作者：
Barrio, Alvaro Martinez;Eriksson, Oskar;Schuster, Jens
通讯作者：
Schuster, Jens
影响因子：
4.4
作者：
Birtle Z;Goodstadt L;Ponting C
通讯作者：
Ponting C
DOI：
10.1073/pnas.0811734106
发表时间：
2009-01-06
影响因子：
11.1
作者：
Alcazar, Ruben;Garcia, Ana V.;Reymond, Matthieu
通讯作者：
Reymond, Matthieu
影响因子：
4.5
作者：
Cai, James J.;Macpherson, J. Michael;Sella, Guy;Petrov, Dmitri A.
通讯作者：
Petrov, Dmitri A.
影响因子：
7
作者：
Bailey, JA;Yavor, AM;Eichler, EE
通讯作者：
Eichler, EE