Development of Allele-Specific Single-Nucleotide Polymorphism-Based Polymerase Chain Reaction Markers in Cytochrome Oxidase I for the Differentiation of Bactrocera papayae and Bactrocera carambolae (Diptera: Tephritidae)

Chua, Tock Hing; Song, Beng Kah; Chong, Yi-Vern

doi:10.1603/ec10169

Cited by 17 publications

(10 citation statements)

References 17 publications

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“…Due to the unresolved clade of B. dorsalis and B. papayae, Boykin et al (2013) concluded that they are the same biological species. A recent study by Chua et al (2010) also successfully differentiates B. carambolae and B. papayae using SNP-PCR analyses. Therefore, these findings disprove the concluding remarks by Drew (1994), which were based on external morphology and declared that the species resembled each other and were no different.…”

Section: Discussionmentioning

confidence: 94%

“…Several Bactrocera species are also known as problematic economic pests that infest and damage a wide variety of crops in Malaysia. The infestation of Bactrocera species consequently reduces production yields and the quality of the crops (Chua et al 2010). Therefore, accurate identification of Bactrocera species is highly important for the successful management of targeted pest and quarantine initiatives (Asokan et al 2011;Liu et al 2011).…”

Section: Introductionmentioning

confidence: 99%

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Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

et al. 2015

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This paper marks the first attempt at using the molecular clock analysis on five Malaysian Bactrocera species based on combined data of COI and ND1 to test the divergence times of species that infested 11 varieties of fruits and vegetables. A divergence tree was constructed to estimate the cryptic species among the five closely related Bactrocera species viz. B. (Bactrocera) and B. (Zeugodacus). Both subgenera evolved and diverged approximately 21.5933 million years ago (MYA). The particularly complex taxonomical status of the sister-species B. papayae and B. carambolae has been resolved using the divergence tree; the two separated from the others approximately 2.743 MYA, while B. papayae and B. carambolae distinctly diverged between 1.9619 and 2.2884 MYA. Additionally, Bactrocera dorsalis showed divergence at 4.1596 MYA and was distinctly separate from the B. papayae. Interestingly, the molecular clock results are congruent with the phylogenetic tree that was analysed using Maximum Parsimony and Bayesian Inference. Further, the taxonomical status and host utilisation of the five Bactrocera species were also briefly discussed, which indicated that B. cucurbitae (subgenus Zeugodacus) was infesting Cucurbitaceae and B. latifrons was infesting Solanaceaea, while B. dorsalis, B. carambolae and B. papaya were infesting a wide range of fruit species. Key message Divergence time of five Malaysian Bactroceran species is reported for the first time and found congruent with the results of phylogeny based on combined data of COI and ND1 markers using MP and Bayesian analyses. This finding could prove very crucial for resolving the most crucial taxonomic conflicts in Bactrocera classification, which is highly important initially in species identification for integrated pest management (IPM) programme.

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Section: Discussionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

et al. 2015

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“…For example, Chua et al . [66] describe an allele-specific diagnostic PCR-assay for Bactrocera carambolae and B . papayae based on COI.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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BackgroundRapid 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.ResultsIn 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.ConclusionsWe 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.

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“…However, this method is time-consuming and costly because of the sequencing process. Some recent studies have used PCR with species-specific primer pairs to make the identification more rapid based only on the presence or absence of a band in the gel profile, thereby overcoming the need for post-amplification digestion and sequencing (Hosseini et al 2007;Chua et al 2010;Zhang et al 2012).…”

Section: Introductionmentioning

confidence: 99%

A rapid diagnostic tool for two species of Tetradacus (Diptera: Tephritidae: Bactrocera) based on species‐specific PCR

Fan

et al. 2013

J Applied Entomology

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Bactrocera minax and Bactrocera tsuneonis are two sibling species of the Bactrocera subgenus Tetradacus with significant quarantine importance in Asia. It is difficult to identify or distinguish them only based on morphological characteristics. In this study, microscopic observations showed that morphological features of adult samples were congruent with the diagnosis of the two species. In this study, we describe species-specific PCR for the molecular identification of B. minax and B. tsuneonis. Species-specific primer pairs were designed on the basis of variations in the mtDNA COI barcode sequences among Bactrocera spp.. A 499 bp-specific fragment of B. minax and a 337 bp absolute product of B. tsuneonis were generated by their respective primer pairs, whilst no such diagnostic bands were present in any of the other fruit fly species tested. The results of the sensitivity test demonstrated that the detection limit of DNA template concentration was 1 ng/ll for B. minax and 0.1 ng/ll for B. tsuneonis. This assay exhibited high specificity, reliability, rapid and low cost for all ontogenetic stages. Our data show that species-specific PCR is a powerful tool that can be used for the identification of B. minax and B. tsuneonis in quarantine work.

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Development of Allele-Specific Single-Nucleotide Polymorphism-Based Polymerase Chain Reaction Markers in Cytochrome Oxidase I for the Differentiation of Bactrocera papayae and Bactrocera carambolae (Diptera: Tephritidae)

Cited by 17 publications

References 17 publications

Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

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

A rapid diagnostic tool for two species of Tetradacus (Diptera: Tephritidae: Bactrocera) based on species‐specific PCR

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