Dataset Information

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.

ABSTRACT: Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems - BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes.

SUBMITTER: Sonet G

PROVIDER: S-EPMC3890684 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.

Sonet Gontran G Jordaens Kurt K Braet Yves Y Bourguignon Luc L Dupont Eréna E Backeljau Thierry T De Meyer Marc M Desmyter Stijn S

ZooKeys 20131230 365

Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calli ...[more]

PMID: 24453564

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Project description:Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

Project description:Flesh flies (Sarcophagidae) are necrophagous insects initially colonizing on a corpse. The species-specific developmental data of the flies collected from a death scene can be used to estimate the minimum postmortem interval (PMImin). Thus, the first crucial step is to correctly identify the fly species. Because of the high similarity among species of flesh flies, DNA-based identification is considered more favorable than morphology-based identification. In this study, we demonstrated the effectiveness of combined sequences (2216 to 2218 bp) of cytochrome c oxidase subunit I and II genes (COI and COII) for identification of the following 14 forensically important flesh fly species in Thailand: Boettcherisca nathani Lopes, Fengia ostindicae (Senior-White), Harpagophalla kempi (Senior-White), Liopygia ruficornis (Fabricius), Lioproctia pattoni (Senior-White), Lioproctia saprianovae (Pape & Bänziger), Parasarcophaga albiceps (Meigen), Parasarcophaga brevicornis (Ho), Parasarcophaga dux (Thomson), Parasarcophaga misera (Walker), Sarcorohdendorfia antilope (Böttcher), Sarcorohdendorfia inextricata (Walker), Sarcorohdendorfia seniorwhitei (Ho) and Seniorwhitea princeps (Wiedemann). Nucleotide variations of Thai flesh flies were evenly distributed throughout the COI-COII genes. Mean intra- and interspecific variations ranged from 0.00 to 0.96% and 5.22% to 12.31%, respectively. Using Best Match (BM) and Best Close Match (BCM) criteria, identification success for the combined genes was 100%, while the All Species Barcodes (ASB) criterion showed 76.74% success. Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic analyses yielded similar tree topologies of monophyletic clades between species with very strong support values. The achieved sequences covering 14 forensically important flesh fly species including newly submitted sequences for B. nathani, F. ostindicae and S. seniorwhitei, can serve as a reliable reference database for further forensic entomological research in Thailand and in other areas where those species occur.

Project description:Background:The time-length between the first colonization of necrophagous insect on the corpse and the beginning of investigation represents the most important forensic concept of minimum post-mortem inference (PMImin). Before colonization, the time spent by an insect to detect and locate a corpse could significantly influence the PMImin estimation. The olfactory system plays an important role in insect food foraging behavior. Proteins like odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors (ORs), ionotropic receptors (IRs) and sensory neuron membrane proteins (SNMPs) represent the most important parts of this system. Exploration of the above genes and their necrophagous products should facilitate not only the understanding of their roles in forging but also their influence on the period before PMImin. Transcriptome sequencing has been wildly utilized to reveal the expression of particular genes under different temporal and spatial condition in a high throughput way. In this study, transcriptomic study was implemented on antennae of adult Aldrichina grahami (Aldrich) (Diptera: Calliphoridae), a necrophagous insect with forensic significance, to reveal the composition and expression feature of OBPs, CSPs, ORs, IRs and SNMPs genes at transcriptome level. Method:Antennae transcriptome sequencing of A. grahami was performed using next-generation deep sequencing on the platform of BGISEQ-500. The raw data were deposited into NCBI (PRJNA513084). All the transcripts were functionally annotated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Differentially expressed genes (DEGs) were analyzed between female and male antennae. The transcripts of OBPs, CSPs, ORs, IRs and SNMPs were identified based on sequence feature. Phylogenetic development of olfactory genes of A. grahami with other species was analyzed using MEGA 5.0. RT-qPCR was utilized to verify gene expression generated from the transcriptome sequencing. Results:In total, 14,193 genes were annotated in the antennae transcriptome based on the GO and the KEGG databases. We found that 740 DEGs were differently expressed between female and male antennae. Among those, 195 transcripts were annotated as candidate olfactory genes then checked by sequence feature. Of these, 27 OBPs, one CSPs, 49 ORs, six IRs and two SNMPs were finally identified in antennae of A. grahami. Phylogenetic development suggested that some olfactory genes may play a role in food forging, perception of pheromone and decomposing odors. Conclusion:Overall, our results suggest the existence of gender and spatial expression differences in olfactory genes from antennae of A. grahami. Such differences are likely to greatly influence insect behavior around a corpse. In addition, candidate olfactory genes with predicted function provide valuable information for further studies of the molecular mechanisms of olfactory detection of forensically important fly species and thus deepen our understanding of the period before PMImin.

Dataset Information

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.

Publications

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.

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