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Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini)

Krosch, M. N., Strutt, F., Blacket, M. J., Batovska, J., Starkie, M., Clarke, A. R., Cameron, S. L. and Schutze, M. K. (2020) Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini). Insect Science, 27 (1). pp. 143-158. ISSN 16729609 (ISSN)

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Article Link(s): https://doi.org/10.1111/1744-7917.12612

Abstract

Accurate species-level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA “barcoding” of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several “universal” COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades-old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the “true” mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species. © 2018 Institute of Zoology, Chinese Academy of Sciences

Item Type:Article
Business groups:Biosecurity Queensland
Keywords:Bactrocera biosecurity Dacus minibarcodes pseudogene Zeugodacus
Subjects:Science > Entomology
Plant pests and diseases > Pest control and treatment of diseases. Plant protection
Animal culture > Insect culture and beneficial insects
Deposited On:21 Oct 2019 23:29
Last Modified:21 Oct 2019 23:29

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