Small Kerrin S, Brudno Michael, Hill Matthew M, Sidow Arend
Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA.
Genome Biol. 2007;8(3):R41. doi: 10.1186/gb-2007-8-3-r41.
The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.
萨氏海鞘（Ciona savignyi）的序列是使用全基因组鸟枪法策略测定的，但高度多态性导致了组装片段化，同一基因组区域的等位基因序列被分别组装。我们设计了一种多步骤策略，通过重建和比对两个“单倍型基因组”（单倍体基因组），从原始组装中生成一个非冗余参考序列。在得到的174兆碱基的参考序列中，每个位点只出现一次，错误组装得到纠正，序列的邻接性和连续性得到显著改善。
