Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation

BMC Evolutionary Biology

Martín Aluja¹  Juan Rull¹  Joerg Samietz²  Beatrice Frey²  Larissa Guillén¹  Juerg E Frey² 

[1] Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México;Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland

关键词: COI;    Cytochrome oxidase I;    Tephritidae;    Quarantine pest insects;    Species delimitation;    Species identification;    Single nucleotide polymorphisms;    Diagnostic SNPs;   

Others  :  1087298
DOI  :  10.1186/1471-2148-13-106

 received in 2012-11-05, accepted in 2013-05-15,  发布年份 2013

【 摘 要 】

Background

Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.

Results

In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.

Conclusions

We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.

【 授权许可】

   
2013 Frey et al.; licensee BioMed Central Ltd.

【 图 表 】

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