Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao.
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.
Cheng
Ting-Cai
TC
The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing 400716, China.
Xia
Qing-You
QY
Qian
Ji-Feng
JF
Liu
Chun
C
Lin
Ying
Y
Zha
Xing-Fu
XF
Xiang
Zhong-Huai
ZH
D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics*; D003062:Codon / Q000235:genetics; D020451:Contig Mapping; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005260:Female; D015723:Gene Library; D008297:Male; D016254:Mutagenesis, Insertional; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017384:Sequence Deletion
D003062:Codon