An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group

Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.

Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors

BACKGROUND

The group of > 40 cryptic whitefly species called Bemisia tabaci sensu lato are amongst the world's worst agricultural pests and plant-virus vectors. Outbreaks of B. tabaci s.l. and the associated plant-virus diseases continue to contribute to global food insecurity and social instability, particularly in sub-Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the 'Ensembl gene annotation system', to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification.

RESULTS

We present here six new B. tabaci s.l. genomes from Africa and Asia, and two re-annotated previously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616-658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform methodology strongly supported a repertoire of between 12.8-13.2 × 10³ PCG. An integrative systematics approach incorporating phylogenomic analysis of nuclear and mitochondrial markers supported a monophyletic Aleyrodidae and the basal positioning of B. tabaci Uganda-1 to the sub-Saharan group of species. Reciprocal cross-mating data and the co-cladogenesis pattern of the primary obligate endosymbiont 'Candidatus Portiera aleyrodidarum' from 11 Bemisia genomes further supported the phylogenetic reconstruction to show that African cassava B. tabaci populations consist of just three biological species. We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. s.l species.

CONCLUSIONS

These genomic resources have provided new and critical insights into the genetics underlying B. tabaci s.l. biology. They also provide a rich foundation for post-genomic research, including the selection of candidate gene-targets for innovative whitefly and virus-control strategies.

Genetic diversity, distribution, and structure of Bemisia tabaci whitefly species in potential invasion and hybridization regions of East Africa

Outbreaks of whitefly, Bemisia tabaci species in East and Central Africa, have become increasingly prevalent during the previous 25 years and are responsible for driving the spread of plant-virus diseases, such as cassava mosaic disease and cassava brown steak disease. Epidemics of these diseases have expanded their ranges over the same period, spreading from Uganda into other sub-Saharan African countries. It was hypothesised that a highly abundant 'invader' population of B. tabaci was responsible for spreading these diseases from Uganda to neighbouring countries and potentially hybridising with the resident cassava B. tabaci populations. Here, we test this hypothesis by investigating the molecular identities of the highly abundant cassava B. tabaci populations from their supposed origin in Uganda, to the northern, central, eastern and coastal regions of Tanzania. Partial mitochondrial cytochrome oxidase I (mtCOI) barcoding sequences and nuclear microsatellite markers were used to analyse the population genetic diversity and structure of 2734 B. tabaci collected from both countries and in different agroecological zones. The results revealed that: (i) the putative SSA1 species is structured according to countries, so differ between them. (ii) Restricted gene flow occurred between SSA1-SG3 and both other SSA1 subgroups (SG1 and SG2), even in sympatry, demonstrating strong barriers to hybridization between those genotypes. (iii) Not only B. tabaci SSA1-(SG1 and SG2) was found in highly abundant (outbreak) numbers, but B. tabaci SSA1-SG3 and the Indian Ocean (IO) species were also recorded in high numbers in several sites in Tanzania. (iv) The SSA1-(SG1 and SG2) species was distributed in both countries, but in Tanzania, the B. tabaci IO and SSA1-SG3 species predominated. These data confirm that multiple, local Tanzanian B. tabaci species produce highly abundant populations, independent of the spread of the putative invasive B. tabaci SSA1-(SG1 and SG2) populations.

Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas

Previous studies in sub-Saharan Africa have showed the spread of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics into different cassava growing regions by high Bemisia tabaci populations. Studies did indicate that there were stark differences in some whitefly species, yet they have not looked extensively across agroecologies. Members of B. tabaci species complex termed sub-Saharan Africa 1 (SSA1) and SSA2 have been linked to the spread of CMD and CBSD viruses. During the period of a severe CMD pandemic in the 1990s, SSA2 was the most predominant until the resurgence of SSA1, particularly SSA1-subgroup1 (SSA1-SG1) from the early 2000s to date. Cassava being a drought resilient crop has become an important food security crop and has been introduced into new areas and regions. Considering the role B. tabaci in the spread of cassava virus pandemics into neighboring regions, we investigated the genetic diversity and distribution of B. tabaci in nine different agro-ecological regions of Uganda in 2017. Adult whiteflies were collected from cassava and 33 other host plants from cassava-growing areas, those with limited cassava and areas with no cassava, where it is being introduced as a food security crop. The partial sequences of the mitochondrial cytochrome oxidase 1 (mtCO1) gene (657 bp) were used to determine the phylogenetic relationships between the sampled B. tabaci. Cassava B. tabaci SSA1 (-SG1, -SG2, -Hoslundia (previously called SSA1-SG1/2), -SG3), SSA2 and SSA3; non-cassava B. tabaci SSA6, SSA10, SSA11, SSA12, SSA13, MED-ASL, MED-Q1, MEAM1, Indian Ocean; and other Bemisia species, Bemisia afer and Bemisia Uganda1 were identified in the study. SSA3, one of the key B. tabaci species that occurs on cassava in West Africa, was identified for the first time in Uganda. The SSA1-SG1 was widely distributed, predominated on cassava and was found on 17 other host-plants. The ability of SSA1-SG1 to exist in environments with limited or no cassava growing poses the risk of continued spread of virus pandemics. Therefore, measures must be put in place to prevent the introduction of diseased materials into new areas, since the vectors exist.

Genetic diversity of whitefly species of the Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) species complex, associated with vegetable crops in Côte d'Ivoire

Since several years, whiteflies of the species complex of Bemisia tabaci (Gennadius) are causing several damages on vegetable crops in Côte d’Ivoire. These sap-sucking insects are the main vector of many viruses on tomato and several species of this complex have developed resistances against insecticides. Nevertheless, there is very little information about whitefly species on vegetable crops in Côte d’Ivoire. Here, we investigated the species diversity and their genetic diversity and structuring on samples from vegetable crops in the major tomato production areas of Côte d’Ivoire. To assess this diversity, 535 whitefly samples from different localities and plant species were collected and analysed with nuclear (microsatellite) and mitochondrial (mtCOI) markers. In each site, and ecological data were recorded, including whiteflies abundance and plant species colonised by B. tabaci. The analysis of mtCOI sequences of whiteflies indicated the presence of four cryptic species on tomato and associated crops in Côte d’Ivoire. These were MED ASL, MED Q1, SSA 1 and SSA3. The MED ASL species dominated over all samples in the different regions and plant species. One haplotype of MED ASL out of the 15 identified predominated on most plant species and most sites. These results suggested that MED ASL is probably the main phytovirus vector in the Ivorian vegetable cropping areas. In contrast, only five haplotypes of MED Q1 were identified on vegetables but in the cotton-growing areas of the country. Its low prevalence, low nuclear and mitochondrial diversity might indicate a recent invasion of this species on vegetable crops in Côte d’Ivoire. The Bayesian nuclear analysis indicated the presence of hybrid genotypes between the two main species MED ASL and MED Q1, however in low prevalence (10%). All these results highlight the need to maintain whitefly populations monitoring for a more effective management in Côte d’Ivoire.

Screening for insecticide resistance in Australian field populations of Bemisia tabaci (Hemiptera: Aleyrodidae) using bioassays and DNA sequencing

BACKGROUND

Species within the Bemisia tabaci cryptic species complex can cause significant crop damage. We used high-throughput amplicon sequencing to identify the species composition and resistance allele genotypes in field populations from cotton fields in Australia. For selected populations, the resistance phenotype was determined in bioassays and compared with sequencing data.

RESULTS

A metabarcoding approach was used to analyse the species composition in 144 field populations collected between 2013 and 2021. Two mixed AUS I and MEAM1 populations were detected, whereas the remaining 142 populations consisted of MEAM1 only. High-throughput sequencing of organophosphate and pyrethroid resistance gene amplicons showed that the organophosphate resistance allele F331W was fixed (> 99%) in all MEAM1 populations, whereas the pyrethroid resistance allele L925I in the voltage-gated sodium channel gene was detected at varying frequencies [1.0%-7.0% (43 populations); 27.7% and 42.1% (two populations); 95%-97.5% (three populations)]. Neither organophosphate nor pyrethroid resistance alleles were detected in the AUS I populations. Pyrethroid bioassays of 85 MEAM1 field-derived populations detected no resistance in 51 populations, whereas 32 populations showed low frequency resistance, and 2 populations were highly resistant.

CONCLUSIONS

We demonstrate that high-throughput sequencing and bioassays are complementary approaches. The detection of target site mutations and the phenotypic provides a comprehensive analysis of the low-level resistance to pyrethroids that is present in Australian cotton farms. By contrast, a limited survey of whitefly populations from horticulture found evidence of high-level resistance against pyrethroids. Furthermore, we found that the F331W allele (linked to organophosphate resistance) is ubiquitous in Australian MEAM1. © 2022 Commonwealth of Australia. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Distribution of invasive versus native whitefly species and their pyrethroid knock-down resistance allele in a context of interspecific hybridization

The invasion success of a species in an agrosystem is greatly influenced by environmental factors such as the use of insecticides, by the intrinsic evolutionary capabilities of the species, and also by interactions with resident species. On the island of La Réunion, the successive invasions of MEAM1 and MED whitefly species over the last 20 years have not only led an increased use of insecticides, but have also challenged the resident IO species. To trace the evolution of the 3 species, and the distribution of the kdr mutation (resistance to pyrethroid) in the para-type voltage-gated sodium channel, we genotyped 41 populations (using neutral nuclear markers) and look at the prevalence of the kdr allele. MEAM1 was predominantly present in agrosystems showing quasi fixation of the resistant kdr allele whereas IO was mainly in natural environments and did not have any resistant allele. Hybridization between the two former species was detected in low frequency but has not led to introgression of resistant alleles in the resident species so far. MED showed a limited distribution in agrosystems but all individuals displayed a resistant allele. These highly contrasting patterns of distribution and resistant mutations between invasive and resident whitefly species are further discussed.

Horizon scanning for prioritising invasive alien species with potential to threaten agriculture and biodiversity in Ghana

Invasive alien species (IAS) continue to shape the global landscape through their effects on biological diversity and agricultural productivity. The effects are particularly pronounced in Sub-Saharan Africa, which has seen the arrival of many IAS in recent years. This has been attributed to porous borders, weak cross border biosecurity, and inadequate capacity to limit or stop invasions. Prediction and early detection of IAS, as well as mechanisms of containment and eradication, are needed in the fight against this global threat. Horizon scanning is an approach that enables gathering of information on risk and impact that can support IAS management. A study was conducted in Ghana to establish two ranked lists of potential invasive alien plant pest species that could be harmful to agriculture, forestry, and the environment, and to rank them according to their potential threat. The ultimate objective was to enable prioritization of actions including pest risk analysis, prevention, surveillance and contingency plans. Prioritisation was carried out using an adapted version of horizon scanning and consensus methods developed for ranking IAS worldwide. Following a horizon scan of invasive alien species not yet officially present in Ghana, a total of 110 arthropod and 64 pathogenic species were assessed through a simplified pest risk assessment. Sixteen species, of which 14 were arthropods and two pathogens, had not been recorded on the African continent at the time of assessment. The species recorded in Africa included 19 arthropod and 46 pathogenic species which were already recorded in the neighbouring countries of Burkina Faso, Côte d’Ivoire, and Togo. The majority of arthropod species were likely to arrive as contaminants on commodities, followed by a sizable number which were likely to arrive as stowaways, while some species were capable of long distance dispersal unaided. The main actions suggested for species that scored highly included full pest risk analyses and, for species recorded in neighbouring countries, surveys to determine their presence in Ghana were recommended.

Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

BACKGROUND

Neonicotinoids are widely applied in the control of the destructive agricultural pest Bemisia tabaci, and resistance against these chemicals has become a common, severe problem in the control of whiteflies. To investigate the molecular mechanism underlying resistance against nenonicotinoids in whiteflies, RNA-seq technology was applied, and the variation in the transcriptomic profiles of susceptible whiteflies and whiteflies selected by imidacloprid, acetamiprid and thiamethoxam treatment was characterized.

RESULTS

A total of 90.86 GB of clean sequence data were obtained from the 4 transcriptomes. Among the 16,069 assembled genes, 584, 110 and 147 genes were upregulated in the imidacloprid-selected strain (IMI), acetamiprid-selected strain (ACE), and thiamethoxam (THI)-selected strain, respectively, relative to the susceptible strain. Detoxification-related genes including P450s, cuticle protein genes, GSTs, UGTs and molecular chaperone HSP70s were overexpressed in the selected resistant strains, especially in the IMI strain. Five genes were downregulated in all three selected resistant strains, including 2 UDP-glucuronosyltransferase 2B18-like genes (LOC 109030370 and LOC 109032577).

CONCLUSIONS

Ten generations of selection with the three neonicotinoids induced different resistance levels and gene expression profiles, mainly involving cuticle protein and P450 genes, in the three selected resistant whitefly strains. The results provide a reference for research on resistance and cross-resistance against neonicotinoids in B. tabaci.

Morphology-based identification of Bemisia tabaci cryptic species puparia via embedded group-contrast convolution neural network analysis

The Bemisia tabaci species complex is a group of tropical–subtropical hemipterans, some species of which have achieved global distribution over the past 150 years. Several species are regarded currently as among the world’s most pernicious agricultural pests, causing a variety of damage types via direct feeding and plant-disease transmission. Long considered a single variable species, genetic, molecular and reproductive compatibility analyses have revealed that this “species” is actually a complex of between 24 and 48 morphologically cryptic species. However, determinations of which populations represent distinct species have been hampered by a failure to integrate genetic/molecular and morphological species–diagnoses. This, in turn, has limited the success of outbreak-control and eradication programs. Previous morphological investigations, based on traditional and geometric morphometric procedures, have had limited success in identifying genetic/molecular species from patterns of morphological variation in puparia. As an alternative, our investigation focused on exploring the use of a deep-learning convolution neural network (CNN) trained on puparial images and based on an embedded, group-contrast training protocol as a means of searching for consistent differences in puparial morphology. Fifteen molecular species were selected for analysis, all of which had been identified via DNA barcoding and confirmed using more extensive molecular characterizations and crossing experiments. Results demonstrate that all 15 species can be discriminated successfully based on differences in puparium morphology alone. This level of discrimination was achieved for laboratory populations reared on both hairy-leaved and glabrous-leaved host plants. Moreover, cross-tabulation tests confirmed the generality and stability of the CNN discriminant system trained on both ecophenotypic variants. The ability to identify B. tabaci species quickly and accurately from puparial images has the potential to address many long-standing problems in B. tabaci taxonomy and systematics as well as playing a vital role in ongoing pest-management efforts. [Aleyrodidae; entomology; Hemiptera; machine learning; morphometrics; pest control; systematics; taxonomy; whiteflies.]

Cytotype Affects the Capability of the Whitefly Bemisia tabaci MED Species To Feed and Oviposit on an Unfavorable Host Plant

The acquisition of nutritional obligate primary endosymbionts (P-symbionts) allowed phloemo-phageous insects to feed on plant sap and thus colonize novel ecological niches. P-symbionts often coexist with facultative secondary endosymbionts (S-symbionts), which may also influence their hosts' niche utilization ability. The whitefly Bemisia tabaci is a highly diversified species complex harboring, in addition to the P-symbiont "Candidatus Portiera aleyrodidarum," seven S-symbionts whose roles remain poorly understood. Here, we compare the phenotypic and metabolic responses of three B. tabaci lines differing in their S-symbiont community, reared on three different host plants, hibiscus, tobacco, or lantana, and address whether and how S-symbionts influence insect capacity to feed and produce offspring on those plants. We first show that hibiscus, tobacco, and lantana differ in their free amino acid composition. Insects' performance, as well as free amino acid profile and symbiotic load, were shown to be plant dependent, suggesting a critical role for the plant nutritional properties. Insect fecundity was significantly lower on lantana, indicating that it is the least favorable plant. Remarkably, insects reared on this plant show a specific amino acid profile and a higher symbiont density compared to the two other plants. In addition, this plant was the only one for which fecundity differences were observed between lines. Using genetically homogeneous hybrids, we demonstrate that cytotype (mitochondria and symbionts), and not genotype, is a major determinant of females' fecundity and amino acid profile on lantana. As cytotypes differ in their S-symbiont community, we propose that these symbionts may mediate their hosts' suitable plant range. IMPORTANCE Microbial symbionts are universal in eukaryotes, and it is now recognized that symbiotic associations represent major evolutionary driving forces. However, the extent to which symbionts contribute to their hosts' ecological adaptation and subsequent diversification is far from being fully elucidated. The whitefly Bemisia tabaci is a sap feeder associated with multiple coinfecting intracellular facultative symbionts. Here, we show that plant species simultaneously affect whiteflies' performance, amino acid profile, and symbiotic density, which could be partially explained by differences in plant nutritional properties. We also demonstrate that, on lantana, the least favorable plant used in our study, whiteflies' performance is determined by their cytotype. We propose that the host plant utilization in B. tabaci is influenced by its facultative symbiont community composition, possibly through its impact on the host dietary requirements. Altogether, our data provide new insights into the impact of intracellular microorganisms on their animal hosts' ecological niche range and diversification.

Whole-genome single nucleotide polymorphism and mating compatibility studies reveal the presence of distinct species in sub-Saharan Africa Bemisia tabaci whiteflies

In sub-Saharan Africa cassava growing areas, two members of the Bemisia tabaci species complex termed sub-Saharan Africa 1 (SSA1) and SSA2 have been reported as the prevalent whiteflies associated with the spread of viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics. At the peak of CMD pandemic in the late 1990s, SSA2 was the prevalent whitefly, although its numbers have diminished over the last two decades with the resurgence of SSA1 whiteflies. Three SSA1 subgroups (SG1 to SG3) are the predominant whiteflies in East Africa and vary in distribution and biological properties. Mating compatibility between SSA1 subgroups and SSA2 whiteflies was reported as the possible driver for the resurgence of SSA1 whiteflies. In this study, a combination of both phylogenomic methods and reciprocal crossing experiments were applied to determine species status of SSA1 subgroups and SSA2 whitefly populations. Phylogenomic analyses conducted with 26 548 205 bp whole genome single nucleotide polymorphisms (SNPs) and the full mitogenomes clustered SSA1 subgroups together and separate from SSA2 species. Mating incompatibility between SSA1 subgroups and SSA2 further demonstrated their distinctiveness from each other. Phylogenomic analyses conducted with SNPs and mitogenomes also revealed different genetic relationships among SSA1 subgroups. The former clustered SSA1-SG1 and SSA1-SG2 together but separate from SSA1-SG3, while the latter clustered SSA1-SG2 and SSA1-SG3 together but separate from SSA1-SG1. Mating compatibility was observed between SSA1-SG1 and SSA1-SG2, while incompatibility occurred between SSA1-SG1 and SSA1-SG3, and SSA1-SG2 and SSA1-SG3. Mating results among SSA1 subgroups were coherent with phylogenomics results based on SNPs but not the full mitogenomes. Furthermore, this study revealed that the secondary endosymbiont-Wolbachia-did not mediate reproductive success in the crossing assays carried out. Overall, using genome wide SNPs together with reciprocal crossings assays, this study established accurate genetic relationships among cassava-colonizing populations, illustrating that SSA1 and SSA2 are distinct species while at least two species occur within SSA1 species.

Biotechnological interventions for the sustainable management of a global pest, whitefly (Bemisia tabaci)

Whiteflies (Bemisia tabaci) are polyphagous invasive hemipteran insects that cause serious losses of important crops by directly feeding on phloem sap and transmitting pathogenic viruses. These insects have emerged as a major threat to global agriculture and food security. Chemically synthesized insecticides are currently the only option to control whiteflies, but the ability of whiteflies to evolve resistance against insecticides has made the management of these insects very difficult. Natural host-plant resistance against whiteflies identified in some crop plants has not been exploited to a great extent. Genetic engineering approaches, such as transgenics and RNA interference (RNAi), are potentially useful for the control of whiteflies. Transgenic plants harboring insecticidal toxins/lectins developed via nuclear or chloroplast transformation are a promising vehicle for whitefly control. Double-stranded RNAs (dsRNAs) of several insect genes, delivered either through microinjection into the insect body cavity or orally via an artificial diet and transiently or stably expressed in transgenic plants, have controlled whiteflies in model plants and in some crops at the laboratory level, but not at the field level. In this review, we highlight the merits and demerits of each delivery method along with strategies for sustained delivery of dsRNAs via fungal entomopathogen/endosymbiont or nontransgenic RNAi approaches, foliar sprays, root absorption or nanocarriers as well as the factors affecting efficient RNAi and their biosafety issues. Genome sequencing and transcriptome studies of whitefly species are facilitating the selection of appropriate genes for RNAi and gene-editing technology for the efficient and resilient management of whiteflies and their transmitted viruses.

Beyond taxonomy: species complexes in New World phlebotomine sand flies

A species complex (= species group, species series) is an assemblage of species, which are related morphologically and phylogenetically. Recent research has revealed several arthropod vector species that were believed to be a single nominal species actually representing a group of closely related species, which are sometimes morphologically indistinguishable at one or more developmental stages. In some instances, differences in terms of vector competence, capacity, or both have been recorded. It highlights the importance of detecting and studying species complexes to improve our understanding of pathogen transmission patterns, which may be vectored more or less efficiently by different species within the complex. Considering more than 540 species, about one-third of the phlebotomine sand flies in the New World present males and/or females morphologically indistinguishable to one or more species. Remarkably, several of these species may act in transmission of pathogenic agents. In this article, we review recent research on species complexes in phlebotomine sand flies from the Americas. Possible practical implications of recently acquired knowledge and future research needs are also discussed.

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host

Background

Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensulato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea.

Results

Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96% were reconstructed. According to ~ 23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria).

Conclusion

Matching genome/transcriptome metrics with the above phylogenetic hypothesis suggests that a haploid nuclear genome of about 50 Mb represents the plesiomorphic state for Rotifera-Acanthocephala. Smaller genome size in S. nebaliae probably results from subsequent reduction. In contrast, genome size should have increased independently in monogononts as well as bdelloid and acanthocephalan stem lines. The present data additionally indicate a decrease in gene repertoire from free-living to epizoic and endoparasitic lifestyles. Potentially, this reflects corresponding steps from the root of Rotifera-Acanthocephala via the last common ancestors of Hemirotifera and Pararotatoria to the one of Acanthocephala. Lastly, rooting via a reconstructed ancestral sequence may prove useful in phylogenetic analyses of other deep splits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07857-y.

Distribution and Genetic Variability of Bemisia tabaci Cryptic Species (Hemiptera: Aleyrodidae) in Italy

Bemisia tabaci is a key pest of horticultural, fibre and ornamental crops worldwide, primarily as a vector of plant viruses. In Italy, B. tabaci has established since the 1980s-1990s in southern regions as well as in Sicily and Sardinia. Recent reports of infestations in some areas of central Italy prompted a new survey to assess the whitefly distribution in the country as well as to update the species and haplotype composition of the populations present in southern Italy and in the main islands. The survey confirmed that B. tabaci is nowadays established in central Italy even at more northern latitudes than those noticed before. Most of the specimens collected throughout the country belonged to the Mediterranean (MED) species. The MEDQ1 and Q2 haplogroups were prevailing in open-field and greenhouse cultivations, respectively, except in Sardinia where only Q1 specimens were found on a wide range of crops and weeds. Population genetics analyses showed that several MEDQ1 haplotypes currently occur in Italy and their distribution is unrelated to evident temporal and geographic trends, except for a new genetic variant which seems to have originated in Sardinia. The MED species is known to better adapt to insecticide treatments and high temperatures, and its northward spread in Italy may have been favoured by the intensive agricultural practices and steady increase in both winter and summer temperatures occurring in the last few decades. The extensive presence of B. tabaci in Italy proves that a strict surveillance for possible new outbreaks of whitefly-transmitted viruses should be addressed to a range of sites that are expanding northwards.

On species delimitation, hybridization and population structure of cassava whitefly in Africa

The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.

Genetic diversity of whitefly (Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa

Over the past three decades, highly increased whitefly (Bemisia tabaci) populations have been observed on the staple food crop cassava in eastern Africa and associated with ensuing viral disease pandemics and food insecurity. Increased whitefly numbers have also been observed in other key agricultural crops and weeds. Factors behind the population surges on different crops and their interrelationships are unclear, although in cassava they have been associated with specific populations within the Bemisia tabaci species complex known to infest cassava crops in Africa. This study carried out an in-depth survey to understand the distribution of B. tabaci populations infesting crops and uncultivated plant hosts in Uganda, a centre of origin for this pest complex. Whitefly samples were collected from 59 identified plant species and 25 unidentified weeds in a countrywide survey. Identities of 870 individual adult whiteflies were determined through mitochondrial cytochrome oxidase 1 sequences (651 bp) in the 3' barcode region used for B. tabaci systematics. Sixteen B. tabaci and five related whitefly putative species were identified based on > 4.0% nucleotide divergence, of which three are proposed as novel B. tabaci putative species and four as novel closely related whitefly species. The most prevalent whiteflies were classified as B. tabaci MED-ASL (30.5% of samples), sub-Saharan Africa 1 (SSA1, 22.7%) and Bemisia Uganda1 (12.1%). These species were also indicated to be the most polyphagous occurring on 33, 40 and 25 identified plant species, respectively. Multiple (≥ 3) whitefly species occurred on specific crops (bean, eggplant, pumpkin and tomato) and weeds (Sida acuta and Ocimum gratissimum). These plants may have increased potential to act as reservoirs for mixed infections of whitefly-vectored viruses. Management of whitefly pest populations in eastern Africa will require an integration of approaches that consider their degree of polyphagy and a climate that enables the continuous presence of crop and uncultivated plant hosts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10340-021-01355-6.

Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives

Simple Summary

Whiteflies are one of the most important and widespread pests in the world. In South America, the currently most important species occurring are Bemisia afer,Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. The present review compiles information from several studies conducted in South America regarding these insects, providing data related to the dynamics and distribution of whiteflies, the associated viruses, and the management strategies to keep whiteflies under the economic damage threshold.

Abstract

By having an extensive territory and suitable climate conditions, South America is one of the most important agricultural regions in the world, providing different kinds of vegetable products to different regions of the world. However, such favorable conditions for plant production also allow the development of several pests, increasing production costs. Among them, whiteflies (Hemiptera: Aleyrodidae) stand out for their potential for infesting several crops and for being resistant to insecticides, having high rates of reproduction and dispersal, besides their efficient activity as virus vectors. Currently, the most important species occurring in South America are Bemisia afer, Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. In this review, a series of studies performed in South America were compiled in an attempt to unify the advances that have been developed in whitefly management in this continent. At first, a background of the current whitefly distribution in South American countries as well as factors affecting them are shown, followed by a background of the whitefly transmitted viruses in South America, addressing their location and association with whiteflies in each country. Afterwards, a series of management strategies are proposed to be implemented in South American fields, including cultural practices and biological and chemical control, finalizing with a section containing future perspectives and directions for further research.

Testing mate recognition through reciprocal crosses of two native populations of the whitefly Bemisia tabaci (Gennadius) in Australia

Bemisia tabaci (Gennadius) represents a relatively large cryptic species complex. Australia has at least two native populations of B. tabaci sensu lato and these were first found on different host plants in different parts of Australia. The species status of these populations has not been resolved, although their mitochondrial sequences differ by 3.82-4.20%. We addressed the question of whether these AUSI and AUSII B. tabaci populations are distinct species. We used reciprocal cross-mating tests to establish whether the insects from these different populations recognize one another as potential mating partners. The results show that the two native Australian populations of B. tabaci have a mating sequence with four phases, each of which is described. Not all pairs in the control crosses mated and the frequency of mating differed across them. Some pairs in the AUSI-M × AUSII-F did mate (15%) and did produce female progeny, but the frequency was extremely low relative to controls. Microsatellite genotyping of the female progeny produced in the crosses showed these matings were successful. None of the AUSII-M × AUSI-F crosses mated although some of the males did search for females. These results demonstrate the critical role of the mate recognition process and the need to assess this directly in cross-mating tests if the species status of different populations is to be tested realistically. In short, AUSI and AUSII B. tabaci populations are distinct species because the individual males and females do not recognize individuals of the alternative population as potential mating partners.

Cassava whitefly species in eastern Nigeria and the threat of vector-borne pandemics from East and Central Africa

Bemisia tabaci (sensu latu) is a group of >40 highly cryptic whitefly species that are of global agricultural importance, both as crop pests and plant-virus vectors. Two devastating cassava diseases in East and Central Africa are spread by abundant populations of one of these species termed Sub-Saharan Africa 1 (SSA1). There is a substantive risk that these whitefly-borne pandemics will continue to spread westwards and disrupt cassava production for millions of smallholder farmers in West Africa. We report here, therefore, the first comprehensive survey of cassava B. tabaci in eastern Nigeria, a West African region likely to be the first affected by the arrival of these whitefly-borne pandemics. We found one haplotype comprising 32 individuals with 100% identical mtCO1 sequence to the East African SSA1 populations (previously termed SSA1-SG1) and 19 mtCO1 haplotypes of Sub-Saharan Africa 3 (SSA3), the latter being the most prevalent and widely distributed B. tabaci species in eastern Nigeria. A more divergent SSA1 mtCO1 sequence (previously termed SSA1-SG5) was also identified in the region, as were mtCO1 sequences identifying the presence of the MED ASL B. tabaci species and Bemisia afer. Although B. tabaci SSA1 was found in eastern Nigeria, they were not present in the high abundances associated with the cassava mosaic (CMD) and cassava brown streak disease (CBSD) pandemics of East and Central Africa. Also, no severe CMD or any CBSD symptoms were found in the region.

A rapid insect species identification system using mini-barcode pyrosequencing

BACKGROUND

Rapid and accurate species identification is not only important for biodiversity studies and pest quarantine and management, but in some cases may also influence the results of international trade negotiations. In this study, we developed a rapid species identification system for insects.

RESULTS

A universal DNA mini-barcode primer pair was designed to target ∼ 120 bp of the mitochondrial 16S rDNA gene. This primer set can amplify the targeted region from all 300 species of 26 insect orders tested as well as other classes of Arthropoda. Although we found no within-species variation in this region, it provided enough information to separate closely related species or species complexes, in particular Thrips spp. and Bemisia spp. By combining a quick DNA extraction method with pyrosequencing, we were able to generate DNA sequences and complete species identification within 5 h.

CONCLUSION

Mini-barcode pyrosequencing of 16S rDNA coupled with the GenBank database provides a rapid, accurate, and efficient species identification system. This system is therefore useful for biodiversity discovery, forensic identification, and quarantine control and management. © 2019 Society of Chemical Industry.

Role of several cytochrome P450s in the resistance and cross-resistance against imidacloprid and acetamiprid of Bemisia tabaci (Hemiptera: Aleyrodidae) MEAM1 cryptic species in Xinjiang, China

Neonicotinoids are commonly used for the control of the whitefly Bemisia tabaci in cotton field. Laboratory test and field experiments have found that whitefly has a high risk of developing resistance and cross-resistance to the pesticide. Over expression of cytochrome P450 is one of the main mechanism that controls pesticide resistance in many insects. In this study we use MEAM1 whitefly, the dominant cryptic species of B. tabaci in Xinjiang cotton field, to investigate the possible resistance and cross-resistance mechanism controlled by cytochrome P450 enzymes. The P450 enzyme activity was higher in both selected strains of imidacloprid and acetamipird than that of susceptible strain. Synergism test showed that piperonyl butoxide (PBO) distinctly increased the control efficiency of imidacloprid and acetamiprid to the two resistance selected strains. Four out of 13 cytochrome genes, CYP4CS3, CYP6CX5, CYP6DW2 and CYP6CM1 were significantly up-regulated in the two selected strains based on real-time fluorescence quantitative PCR results. Other 3 genes, CYP6CX2, CYP6CX4 and CYP6DW3 were only highly expressed in the acetamiprid selected strain instead of the susceptible strain and imidacloprid selected strain. CYP6CM1 showed the highest expression level among all the 13 tested genes. No functional mutation of CYP6CM1 was found by sequence analysis. The possible role of these genes involving the resistance and cross-resistance of the whitefly MEAM1 cryptic species against neonicotinoids was discussed.

Genomic biosurveillance of forest invasive alien enemies: A story written in code

The world's forests face unprecedented threats from invasive insects and pathogens that can cause large irreversible damage to the ecosystems. This threatens the world's capacity to provide long-term fiber supply and ecosystem services that range from carbon storage, nutrient cycling, and water and air purification, to soil preservation and maintenance of wildlife habitat. Reducing the threat of forest invasive alien species requires vigilant biosurveillance, the process of gathering, integrating, interpreting, and communicating essential information about pest and pathogen threats to achieve early detection and warning and to enable better decision-making. This process is challenging due to the diversity of invasive pests and pathogens that need to be identified, the diverse pathways of introduction, and the difficulty in assessing the risk of establishment. Genomics can provide powerful new solutions to biosurveillance. The process of invasion is a story written in four chapters: transport, introduction, establishment, and spread. The series of processes that lead to a successful invasion can leave behind a DNA signature that tells the story of an invasion. This signature can help us understand the dynamic, multistep process of invasion and inform management of current and future introductions. This review describes current and future application of genomic tools and pipelines that will provide accurate identification of pests and pathogens, assign outbreak or survey samples to putative sources to identify pathways of spread, and assess risk based on traits that impact the outbreak outcome.

First Evidence of Intracellular Bacteria Cardinium in Thermophilic Mite Microzetorchestes emeryi (Acari: Oribatida): Molecular Screening of Bacterial Endosymbiont Species

We undertook the issue of the distribution of intracellular bacteria among Oribatida (Acari). Six genera of bacteria were detected by PCR and Sanger DNA sequencing: Wolbachia, Cardinium, Rickettsia, Spiroplasma, Arsenophonus, and Hamiltonella. Our research, for the first time, revealed the presence of Cardinium in Microzetorchestes emeryi in two subpopulations separated from each other by 300 m. The percentages of infected animals were the same in both subpopulations-ca. 20%. The identity of 16S rDNA sequences of Cardinium between these two subpopulations of M. emeryi was 97%. Phylogenetic analysis showed that the Cardinium in M. emeryi was clustered into the group A. The occurrence of M. emeryi in Poland has not been reported before and our report is the first one. Cardinium maybe help the thermophilic M. emeryi to adapt to low temperatures in the Central Europe.

Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species

Background

Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic species that differ from each other in many characteristics such as mode of interaction with viruses, invasiveness, and resistance to insecticides. Asia II 1 is an indigenous species found on the Indian sub-continent and south-east Asia while the species named as Middle East Asia Minor 1 (MEAM1), likely originated from the Middle-East and has spread worldwide in recent decades. The purpose of this study is to find genomic differences between these two species.

Results

Sequencing of the nuclear genome of Asia II 1 with Illumina HiSeq and MiSeq generated 198.90 million reads that covers 88% of the reference genome. The sequence comparison with MEAM1 identified 2,327,972 SNPs and 202,479 INDELs. In Total, 1294 genes were detected with high impact variants. The functional analysis revealed that some of the genes are involved in virus transmission including 4 genes in Tomato yellow leaf curl virus (TYLCV) transmission, 96 in Tomato crinivirus (ToCV) transmission, and 14 genes in insecticide resistance.

Conclusions

These genetic differences between Asia II 1 and MEAM1 may underlie the major biological differences between the two species such as virus transmission, insecticide resistance, and range of host plants. The present study provides new genomic data and information resources for Asia II 1 that will not only contribute to the species delimitation of whitefly, but also help in conceiving future research studies to develop more targeted management strategies against whitefly.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5877-9) contains supplementary material, which is available to authorized users.

Going global - genomic insights into insect invasions

The spread of invasive insect pests is becoming an increasing problem for agriculture globally. We discuss a number of invasive insects, already of major economic significance that have recently expanded their range to become truly global threats. These include the noctuid moths Helicoverpa and Spodoptera, whose caterpillars have long been among the worst pests in their native Old and New World habitats, respectively, and the whitefly Bemisia, a major vector of plant virus diseases. Importantly, genomic resources for these species have recently become available, allowing research to move beyond the restrictions imposed by earlier approaches limited to a single or few mitochondrial and nuclear markers, to employ genome-wide genotyping and resequencing protocols. These studies have shown hybridisation within the various species complexes, identified regions under selection in agricultural environments, and enable monitoring of genes important as biosecurity risks through introgression into established populations free of the genes. In all cases studied, global trade has emerged as the probable cause of insect spread, making it ever more important that biosecurity protocols and agencies work with researchers to make the most effective use of emerging genomic resources and tools.