Cheng Ting-Cai, Xia Qing-You, Qian Ji-Feng, Liu Chun, Lin Ying, Zha Xing-Fu, Xiang Zhong-Huai
The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing 400716, China.
Insect Biochem Mol Biol. 2004 Jun;34(6):523-30. doi: 10.1016/j.ibmb.2004.02.004.
We made use of 81,635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of the silkworm, Bombyx mori, inbred strain Dazao (P50), to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, 12,980 contigs containing 11,537 contigs assembled by more than one read were obtained, and 101 candidate SNPs and 27 single base insertions/deletions were identified from 117 contigs assembled from 1576 high-quality reads base-called with PHRED and screened on the basis of the neighborhood quality standard (NQS). Simultaneously, we also predicted 40 SNPs in coding regions (cSNPs), of which 26 were predicted to lead to amino acid non-synonymous variations and 14 synonymous substitutions. Also, the 1.66:1 ratio of transition/transversion is different from that of other insects. As the first SNP analysis of a Lepidoptera, B. mori, the single nucleotide polymorphic density is estimated to be 1.3 x 10(-3) by sequence diversity. This analysis shows that expressed sequences from multiple libraries may provide an abundant source of comparative reads to mine for cSNPs from the silkworm genome.
我们利用了来自家蚕（Bombyx mori）近交系大造（P50）的12个不同cDNA文库的81,635个表达序列标签（EST）来鉴定高质量的候选单核苷酸多态性（SNP）。通过PHRAP组装，获得了12,980个重叠群，其中包含由多个reads组装而成的11,537个重叠群，并且从117个重叠群中鉴定出101个候选SNP和27个单碱基插入/缺失，这些重叠群由PHRED进行碱基识别的1576个高质量reads组装而成，并根据邻域质量标准（NQS）进行筛选。同时，我们还预测了编码区中的40个SNP（cSNP），其中26个预计会导致氨基酸非同义变异，14个为同义替换。此外，转换/颠换的1.66:1比例与其他昆虫不同。作为对鳞翅目家蚕的首次SNP分析，通过序列多样性估计单核苷酸多态性密度为1.3×10^(-3)。该分析表明，来自多个文库的表达序列可能为从家蚕基因组中挖掘cSNP提供丰富的比较reads来源。
