Assembly of polymorphic genomes:: Algorithms and application to Ciona savignyi
Assembly of polymorphic genomes:: Algorithms and application to Ciona savignyi
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DOI：
10.1101/gr.3722605
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发表时间：
2005-08-01
期刊：
影响因子：
7
通讯作者：
Lander, ES
中科院分区：
文献类型：
--
作者：
Vinson, JP;Jaffe, DB;Lander, ES
全基因组组装现在通常用于获得具有低多态性水平的物种基因组的高质量草图序列。然而，对于高度多态性的物种，基因组组装仍然极具挑战性。困难的出现是因为两个不同的单倍型是在一起测序的，这使得很难区分同一位点的等位基因和不同位点的同源基因。我们提出了一种组装高度多态二倍体基因组的方法，该方法包括分别组装两个单倍型，然后将它们合并以获得参考序列。我们的方法用于组装海鞘Ciona savignyi的基因组，该基因组测序深度为12.7x，来自单个野生个体。通过比较两个单倍型的完成克隆，我们确定测序个体具有极高的杂合率，平均为4.6%，具有显著的区域差异和所有物理尺度上的重排。应用这些数据，我们的方法产生了一个覆盖157 Mb的参考汇编，其中N50 contig和scaffold的大小分别为47 kb和989 kb。ESTs比对表明88%的基因座在参考序列中至少出现一次，81%的基因座恰好出现一次。我们的方法比传统的全基因组组装方法更可靠地表示单个拷贝中的位点，并且实现了更大的连续性。
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging for highly polymorphic species. The difficulty arises because two divergent haplotypes are sequenced together, making it difficult to distinguish alleles at the same locus from paralogs at different loci. We present here a method for assembling highly polymorphic diploid genomes that involves assembling the two haplotypes separately and then merging them to obtain a reference sequence. Our method was developed to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7x from a single wild individual. By comparing finished clones of the two haplotypes we determined that the sequenced individual had ail extremely high heterozygosity rate, averaging 4.6% with significant regional variation and rearrangements at all physical scales. Applied to these data, Our method produced a reference assembly covering 157 Mb, with N50 contig and scaffold sizes of 47 kb and 989 kb, respectively. alignment of ESTs indicates that 88% of loci are present at least once and 81% exactly once in the reference assembly. Our method represented loci in a single copy more reliably and achieved greater Contiguity than a conventional whole-genome assembly method.