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Developing a MtSNP-based genotyping system for genetic identification of forensically important flesh flies (Diptera: Sarcophagidae)

Chen, Wei, Shang, Yanjie, Ren, Lipin, Xie, Kai, Zhang, Xiangyan, Zhang, Changquan, Sun, Shule, Wang, Yong, Zha, Lagabaiyila, Guo, Yadong
Forensic science international 2018 v.290 pp. 178-188
DNA barcoding, Sarcophagidae, cost effectiveness, cytochrome-c oxidase, death, genetic variation, genotyping, memory, mitochondrial genes, polymerase chain reaction, postmortem changes, single nucleotide polymorphism, species identification
Some representatives of flesh flies visiting/colonizing the decomposed remains demonstrated their values in estimating the minimal postmortem interval (PMImin) since death. However, the utility of sarcophagid flies has been seriously hampered by limited ecological, biological and taxonomic knowledge of them. Although mitochondrial genes have been proposed as a potential DNA barcode for the species-level identification of sarcophagids, some defects still remain such as the substantial memory and processing time taken for homologous comparisons online. Moreover, species identification is mainly achieved by Sanger sequencing based on PCR with genus-specific primers. In the present study we characterized 24 single nucleotide polymorphisms (SNPs) as robust markers of genetic variation for identifying different sarcophagids based on available cytochrome c oxidase I (COI) data and verified them through pyrosequencing (PSQ) technology to establish a SNP-based genotyping system. The system provides a preliminary foundation for developing a rapid, reliable, and high-throughput assay so as to efficiently and accurately identify the sarcophgid flies. Furthermore, the PSQ approach is proved to be faster, more cost-effective as well as more sensitive and specific than custom Sanger sequencing.