Sequencing of natural strains of Arabidopsis thaliana with short reads
Sequencing of natural strains of Arabidopsis thaliana with short reads
复制标题
DOI：
10.1101/gr.080200.108
复制
发表时间：
2008-12-01
期刊：
影响因子：
7
通讯作者：
Weigel, Detlef
中科院分区：
文献类型：
--
作者：
Ossowski, Stephan;Schneeberger, Korbinian;Weigel, Detlef
全基因组杂交研究表明，拟南芥（Arabidopsis thaliana）的核基因组可以在它们的序列上有百分之几的差异。为了检查这种变异，并且作为该物种的1001基因组计划的第一步，我们在Illumina合成测序（SBS）读数中为参考登录号Col-0和两种不同菌株Bur-0和大津-1产生了15至25倍的覆盖率。我们将读数与参考基因组序列进行比对，以评估数据质量指标并检测多态性。比对结果显示，在特异性> 99%的不同种质中有823，325个独特的单核苷酸多态性（SNP）和79，961个独特的1-至3-bp indel，并且在参考基因组序列中有超过2000个潜在错误。我们还鉴定了>3.4 Mb的Bur-0和大津-1基因组相对于参考基因组是极不相似的、缺失的或重复的。为了获得这些区域的序列，我们将Velvet组装程序整合到靶向从头组装方法中。这种方法产生了10，921个高置信度的重叠群，这些重叠群锚定到侧翼序列上，并含有高达641 bp的插入缺失。我们的方法广泛适用于中大型基因组中的多态性发现，即使在高度分歧的基因座，我们通过子采样建立了Illumina SBS覆盖深度，以告知广泛的功能和进化研究。我们用于比对读段和预测SNP和indel的管道海岸可在http://1001genomes.org下载。
Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence. To examine this variation, and as a first step in the 1001 Genomes Project for this species, we produced 15- to 25-fold coverage in Illumina sequencing-by-synthesis (SBS) reads for the reference accession, Col-0, and two divergent strains, Bur-0 and Tsu-1. We aligned reads to the reference genome sequence to assess data quality metrics and to detect polymorphisms. Alignments revealed 823,325 unique single nucleotide polymorphisms (SNPs) and 79,961 unique 1- to 3-bp indels in the divergent accessions at a specificity of >99%, and over 2000 potential errors in the reference genome sequence. We also identified >3.4 Mb of the Bur-0 and Tsu-1 genomes as being either extremely dissimilar, deleted, or duplicated relative to the reference genome. To obtain sequences for these regions, we incorporated the Velvet assembler into a targeted de novo assembly method. This approach yielded 10,921 high-confidence contigs that were anchored to flanking sequences and harbored indels as large as 641 bp. Our methods are broadly applicable for polymorphism discovery in moderate to large genomes even at highly diverged loci, and we established by subsampling the Illumina SBS coverage depth required to inform a broad range of functional and evolutionary studies. Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org.