Phylogenomic resolution of the Ceratitis FARQ complex (Diptera: Tephritidae)

Distribution and host ranges of Ceratitis rosa and Ceratitis quilicii (Diptera: Tephritidae) in South Africa

Two fruit fly (Diptera: Tephritidae) species of economic importance: Ceratitis rosa Karsch and Ceratitis quilicii De Meyer, Mwatawala & Virgilio are present in South Africa. The two species were considered as one species prior to 2016, but were subsequently separated. In this study, the distribution and abundance of the two species were quantified in seven provinces in South Africa through trapping with Enriched Ginger Oil as an attractant. Trapping was conducted over three seasons across two years (2020 and 2021): late summer, autumn-winter, and spring-early summer. Host ranges of the two species were investigated by fruit sampling in and outside of trapping sites. Ceratitis quilicii was more widely distributed than C. rosa with the latter being recorded in only three north-eastern provinces. There were geographical limits for both species with no records of them in Northern Cape Province. Catches of C. quilicii were higher in summer with average temperatures varying from 15 to 27°C while for C. rosa, catches remained low and consistent between seasons. Ceratitis quilicii catches decreased at lower rates than those of C. rosa at temperatures below 15°C. The two species were reared from 13 plant species from nine families. Four of these hosts were infested by both C. quilicii and C. rosa in the same province where they occurred. Preferred hosts of the two species belonged to the Myrtaceae family. The characterisation of the distribution, abundance and host ranges of these pests will provide a baseline for pest status determination and implementation of management actions.

Phylogenomic analysis and molecular identification of true fruit flies

The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.

Loop-mediated isothermal amplification of economically important Ceratitis species (Diptera: Tephritidae)

Ceratitis is an economically important genus of fruit flies that originated in Africa, has a wide host range, and causes serious economic losses due to its invasive damage. As a result, it is critical to identify them accurately and quickly in the world. Loop-mediated isothermal amplification (LAMP), as one of the representatives of isothermal amplification technology, has been widely used in the rapid nucleic acid detection of human pathogens and has shown its advantages in the identification of insect agricultural pests. In this study, using the mitochondrial cox1 and cob genes as target genes, the rapid molecular identification of the Ceratitis FARQ complex, C. cosyra, and C. capitata was realized based on LAMP. The experimental conditions optimization results showed that F3/B3:FIP/BIP = 1:8 was the optimal primer concentration ratio and 63 °C was the optimal reaction temperature. The sensitivity of the primers obtained in this study can reach up to 0.01 ng/μl DNA. A loop-mediated isothermal amplification identification technology system was established based on rapid, rough DNA extraction and visual detection of Ceratitis economically important fruit flies. The positive reaction system changed from pink to khaki by visual detection. The identification flow can be completed within 1 hour, including sample processing, DNA extraction, and LAMP visual detection.

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole-genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome-scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.

A comparative analysis of the chromosomes of three FARQ species complex members, Ceratitis rosa, C. quilicii, and C. fasciventris F2 (Diptera: Tephritidae)

The Ceratitis FARQ species complex consists of four highly destructive agricultural pests of Africa, namely C. fasciventris, C. anonae, C. rosa, and C. quilicii. The members of the complex are considered very closely related and the species limits among them are rather obscure. Their economic significance and the need for developing biological methods for their control makes species identification within the complex an important issue, which has become clear that can only be addressed by multidisciplinary approaches. Chromosomes, both mitotic and polytene, can provide a useful tool for species characterization and phylogenetic inference among closely related dipteran species. In the current study, we present the mitotic karyotype and the polytene chromosomes of C. rosa and C. quilicii together with in situ hybridization data. We performed a comparative cytogenetic analysis among the above two species and C. fasciventris, the only other cytogenetically studied member of the FARQ complex, by comparing the mitotic complement and the banding pattern of the polytene chromosomes of each species to the others, as well as by studying the polytene chromosomes of hybrids between them. Our analysis revealed no detectable chromosomal rearrangements discriminating the three FARQ members studied, confirming their close phylogenetic relationships.

Utilisation of a mitochondrial intergenic region for species differentiation of fruit flies (Diptera: Tephritidae) in South Africa

BACKGROUND

Fruit flies (Diptera: Tephritidae) comprise species of agricultural and economic importance. Five such fruit fly species are known to affect commercial fruit production and export in South Africa: Ceratitis capitata, Ceratitis cosyra, Ceratitis rosa, Ceratitis quilicii, and Bactrocera dorsalis. Management practices for these pests include monitoring, application of pest control products, post-harvest disinfestation measures and inspection of consignments both prior to shipment and at ports of entry. In activities relating to monitoring and inspection, accurate identification of these pests to species level is required. While morphological keys for adult stages of these fruit fly species have been well developed, morphological keys for earlier life stages remain problematic. In instances where closely related species cannot be reliably distinguished morphologically, there is a need for molecular tools to assist in identifying these five fruit fly species during surveillance practices, where sequencing-based approaches would be beneficial.

RESULTS

Two complete mitochondrial genomes were assembled for each fruit fly species investigated using high throughput sequencing data generated in this study. A single primer set was designed to amplify a region between tRNAile and tRNAmet. The amplicon consists of a partial segment of tRNAile, intergenic region I (tRNAile - tRNAgln), the complete sequence of tRNAgln, intergenic region II (tRNAgln - tRNAmet), and a partial segment of tRNAmet. PCR amplicons were generated for 20 specimens of each species, five of which were colony adult males, five colony larvae, and 10 wild, trap-collected specimens. Upon analysis of the amplicon, intergenic region I was identified as the most informative region, allowing for unambiguous identification of the five fruit fly species. The similarity in intergenic region II was too high between C. rosa and C. quilicii for accurate differentiation of these species.

CONCLUSION

The identity of all five fruit flies investigated in this study can be determined through sequence analysis of the mitochondrial intergenic regions. Within the target amplicon, intergenic region I (tRNAile - tRNAgln) shows interspecific variation sufficient for species differentiation based on multiple sequence alignment. The variation in the length of intergenic region I is proposed as a potential tool for accurately identifying these five fruit flies in South Africa.

A multiplex PCR assay for the identification of fruit flies (Diptera: Tephritidae) of economic importance in South Africa

The fruit fly (Diptera: Tephritidae) species, Ceratitis capitata, Ceratitis cosyra, Ceratitis rosa, Ceratitis quilicii, and Bactrocera dorsalis are of economic importance in South Africa. These agricultural pests cause extensive damage to a range of commercially produced fruit, primarily for export. These pests are of phytosanitary significance, and their presence in fruit-producing regions in South Africa has led to restrictions in export trade of fresh produce. Accurate identification of these flies, particularly at immature stages intercepted in fruit consignments originating from South Africa, is essential but remains an ongoing challenge. A rapid and accurate identification assay to differentiate these five species is needed for inspection and pest surveillance. High throughput sequencing data were generated for each of the five fruit fly species, and five sets of species-specific primers were designed for use in a multiplex PCR. Each primer set amplifies an amplicon of a different size for each species allowing for accurate identification. PCR sensitivity tests demonstrate that the limit of detection for this assay is 10 ng and 4 ng of DNA when extracted from larvae and adult specimens, respectively. The assay developed can be applied in fruit inspection and survey activities within the country and at ports of entry.

Predicting the Invasion Risk by Anastrepha sororcula (Diptera: Tephritidae) in Distinct Geographic Regions

The movement of endemic fruit flies to new habitats represents a major biological and economic threat. Anastrepha sororcula Zucchi, 1979 is widely distributed in Brazil and also in Colombia, Ecuador, and Paraguay. Here, we present the potential distribution of A. sororcula in endemic areas and project this model into other regions such as part of sub-Saharan Africa, Central America, and Asia to show areas around the world that this species can potentially establish. We combined geographic coordinates with climate data. The models were built using the maximum entropy (MaxEnt) algorithm. Many mango- and guava-producing countries exhibited climatic suitability for A. sororcula in the regions studied including the nine largest world producers: India, Brazil, Malawi, Kenya, Haiti, Cuba, Colombia, Madagascar, and the Democratic Republic of the Congo. Many of these countries showed ideal host plant availability and climatic conditions for the entry and establishment of A. sororcula. This study is a pioneer in the identification of representative areas in the world with climatic suitability for A. sororcula, which shows the importance of predicting areas at risk of invasion to monitor the movement and establishment of fruit fly species in new regions, which is fundamental to area-wide integrated pest management programs.