DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan

Diversity study of Beauveria bassiana species for finding the most virulent strain to manage Bemisia tabaci in cotton

Beauveria bassiana (Bal.-Criv.) is an important entomopathogenic fungus being used for the management of various agricultural pests worldwide. However, all strains of B. bassiana may not be effective against whitefly, Bemisia tabaci, or other pests, and strains show diversity in their growth, sporulation, virulence features, and overall bioefficacy. Thus, to select the most effective strain, a comprehensive way needs to be devised. We studied the diversity among the 102 strains of B. bassiana isolated from 19 insect species based on their physiological features, virulence, and molecular phylogeny, to identify promising ones for the management of B. tabaci. Strains showed diversity in mycelial growth, conidial production, and their virulence against B. tabaci nymphs. The highest nymphal mortality (2nd and 3rd instar) was recorded with MTCC-4511 (95.1%), MTCC-6289 (93.8%), and MTCC-4565 (89.9%) at a concentration of 1 × 106 conidia ml-1 under polyhouse conditions. The highest bioefficacy index (BI) was in MTCC-4511 (78.3%), MTCC-4565 (68.2%), and MTCC-4543 (62.1%). MTCC-4511, MTCC-4565, and MTCC-4543 clustered with positive loading of eigenvalues for the first two principal components and the cluster analysis also corresponded well with PCA (principal component analysis) (nymphal mortality and BI). The molecular phylogeny could not draw any distinct relationship between physiological features, the virulence of B. bassiana strains with the host and location. The BI, PCA, and square Euclidean distance cluster were found the most useful tools for selecting potential entomopathogenic strains. The selected strains could be utilized for the management of the B. tabaci nymphal population in the field through the development of effective formulations. KEY POINTS: • 102 B. bassiana strains showed diversity in growth and virulence against B. tabaci. • Bioefficacy index, PCA, and SED group are efficient tools for selecting potential strains. • MTCC-4511, 4565, and 4543 chosen as the most virulent strains to kill whitefly nymphs.

Diversity and functional characteristics of culturable bacterial endosymbionts from cassava whitefly biotype Asia II-5, Bemisia tabaci

Whitefly Bemisia tabaci, a carrier of cassava mosaic disease (CMD), poses a significant threat to cassava crops. Investigating culturable bacteria and their impact on whiteflies is crucial due to their vital role in whitefly fitness and survival. The whitefly biotype associated with cassava and transmitting CMD in India has been identified as Asia II 5 through partial mitochondrial cytochrome oxidase I gene sequencing. In this study, bacteria associated with adult B. tabaci feeding on cassava were extracted using seven different media. Nutrient Agar (NA), Soyabean Casein Digest Medium (SCDM), Luria Bertani agar (LBA), and Reasoner's 2A agar (R2A) media resulted in 19, 6, 4, and 4 isolates, respectively, producing a total of 33 distinct bacterial isolates. Species identification through 16SrRNA gene sequencing revealed that all isolates belonged to the Bacillota and Pseudomonadota phyla, encompassing 11 genera: Bacillus, Cytobacillus, Exiguobacterium, Terribacillus, Brevibacillus, Enterococcus, Staphylococcus, Brucella, Novosphingobium, Lysobacter, and Pseudomonas. All bacterial isolates were tested for chitinase, protease, siderophore activity, and antibiotic sensitivity. Nine isolates exhibited chitinase activity, 28 showed protease activity, and 23 displayed siderophore activity. Most isolates were sensitive to antibiotics such as Vancomycin, Streptomycin, Erythromycin, Kanamycin, Doxycycline, Tetracycline, and Ciprofloxacin, while they demonstrated resistance to Bacitracin and Colistin. Understanding the culturable bacteria associated with cassava whitefly and their functional significance could contribute to developing effective cassava whitefly and CMD control in agriculture.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03949-0.

Phylogeography, genetic diversity, and intraspecific genetic structure of the black-horned capuchin (Sapajus nigritus)

Recent molecular studies have clarified the overarching taxonomy of capuchin monkeys, but intraspecific genetic diversity remains unexplored for most capuchin species. One example is Sapajus nigritus, the southernmost capuchin monkey, found in Brazil and Argentina; its phenotypic diversity has been recognized as two geographic subspecies, but the intraspecific genetic structure of this taxon is poorly known. Here, we sampled across most of this species' geographic distribution, producing a newly sequenced data set for genetic analyses that included 78 individuals from 14 populations. We investigated the intraspecific diversity, genetic structure, and evolutionary history using three mitochondrial markers. Our results indicated that S. nigritus populations exhibited high levels of genetic structure. We found strong support for two monophyletic clades within this species with a deep phylogenetic split, and clear separation from other related taxa. Vicariance events seem to have played a prevalent role in shaping S. nigritus genetic differentiation. The Paraíba do Sul River may have driven the deep divergence between southern and northern clades, whereas the Tietê River may have had a weaker, more recent effect on the divergence of populations within the southern clade.

Conservation Genetics of the Critically Endangered Southern River Terrapin (Batagur affinis) in Malaysia: Genetic Diversity and Novel Subspecies Distribution Ranges

A population genetics study was carried out on the Southern River terrapin (Batagur affinis) from four places in Peninsular Malaysia: Pasir Gajah, Kemaman (KE), Terengganu; Bukit Pinang (BP), Kedah; Bota Kanan (BK), Perak; and Bukit Paloh, Kuala Berang (KB), Terengganu. The goal of this study is to identify genetic differences in two subspecies of B. affinis in Malaysia. No previous reports were available on the genetic diversity, phylogenetic relationships and matrilineal hereditary structure of these terrapin populations in Malaysia. The sequencing identified 46 single nucleotide polymorphisms that defined six mitochondrial haplotypes in the Southern River terrapins. Tajima’s D test and Fu’s Fs neutrality tests were performed to evaluate the signatures of recent historical demographic events. Based on the tests, the B. affinis edwardmolli was newly subspecies identified in the west coast–northern region of Kedah state. In addition, the B. affinis edwardmolli in Bukit Paloh, Kuala Berang (KB), Terengganu (Population 4), was shown to have a single maternal lineage compared to other populations. Low genetic diversity, but significant genetic differences, were detected among the studied Southern River terrapin populations.

Comparative transcriptome profiling reveals a network of differentially expressed genes in Asia II 7 and MEAM1 whitefly cryptic species in response to early infection of Cotton leaf curl Multan virus

Cotton leaf curl Multan virus (CLCuMuV) is a whitefly-vectored begomovirus that poses ramping threat to several economically important crops worldwide. The differential transmission of CLCuMuV by its vector Bemisia tabaci mainly relies on the type of whitefly cryptic species. However, the molecular responses among different whitefly cryptic species in response to early CLCuMuV infection remain elusive. Here, we compared early-stage transcriptomic profiles of Asia II 7 and MEAM1 cryptic species infected by CLCuMuV. Results of Illumina sequencing revealed that after 6 and 12 h of CLCuMuV acquisition, 153 and 141 genes among viruliferous (VF) Asia II 7, while 445 and 347 genes among VF MEAM 1 whiteflies were differentially expressed compared with aviruliferous (AVF) whiteflies. The most abundant groups of differentially expressed genes (DEGs) among Asia II 7 and MEAM1 were associated with HTH-1 and zf-C2H2 classes of transcription factors (TFs), respectively. Notably, in contrast to Asia II 7, MEAM1 cryptic species displayed higher transcriptional variations with elevated immune-related responses following CLCuMuV infection. Among both cryptic species, we identified several highly responsive candidate DEGs associated with antiviral innate immunity (alpha glucosidase, LSM14-like protein B and phosphoenolpyruvate carboxykinase), lysosome (GPI-anchored protein 58) and autophagy/phagosome pathways (sequestosome-1, cathepsin F-like protease), spliceosome (heat shock protein 70), detoxification (cytochrome P450 4C1), cGMP-PKG signaling pathway (myosin heavy chain), carbohydrate metabolism (alpha-glucosidase), biological transport (mitochondrial phosphate carrier) and protein absorption and digestion (cuticle protein 8). Further validation of RNA-seq results showed that 23 of 28 selected genes exhibited concordant expression both in RT-qPCR and RNA-seq. Our findings provide vital mechanistic insights into begomovirus-whitefly interactions to understand the dynamics of differential begomovirus transmission by different whitefly cryptic species and reveal novel molecular targets for sustainable management of insect-transmitted plant viruses.

Evaluation of the Bioefficacy and Insecticide Compatibility of Entomopathogens for Management of Whitefly (Hemiptera: Aleyrodidae) on Upland Cotton Under Laboratory and Polyhouse Conditions

Entomopathogens (EPFs) are potential alternatives to chemical insecticides for managing Bemisia tabaci (Genn.), an invasive pest of the cotton crop. EPFs alone may not always provide enough insect pest control, but combining EPFs with pesticides, provided both components are compatible, can make an integrated pest management program considerably more effective. Hence, the bioefficacy of EPFs against whitefly, their compatibility with pesticides, and the factors responsible for determining compatibility were studied. The highest nymphal mortality was recorded with the Beauveria bassiana strains Bb-4511 (95.1%) and Bb-4565 (89.9%), and Metarhizium anisopliae Ma-1299 (86.7%) at 1 × 10⁶ conidia ml^-1. Lower LC₅₀ values were observed for Cordyceps javanica Cj-089 and Bb-4511, 0.2 × 10⁴ and 0.5 × 10⁴ conidia ml^-1, respectively. The toxicity index values in insecticide sensitivity assays ranged from 19.4 to 119.6% among all the EPFs. Comparatively, all the EPFs except Bb-4543 and Bb-4565 showed compatible to moderately toxic reactions to neonicotinoids and spinosyns. Organophosphates (ethion) and pyrethrins (bifenthrin) were toxic to very toxic to all the EPFs except Bb-4511, Fv-083, and Ma-1299. Cj-102 and Cj-089 were compatible with 50% of the average recommended dose of bifenthrin and ethion, and the average recommended dose for the field application of neonicotinoids and spinosyns. Principal component analysis showed that spore production and toxicity index values correlate with each other and are responsible for determining the EPF compatibility with insecticides. The EPF spore production and toxicity index are important factors for determining chemical compatibility. Compatible EPFs can be used individually or in combination as promising and compatible biological alternatives to insecticides in the management of whitefly in cotton.

Pervasive Endosymbiont Arsenophonus Plays a Key Role in the Transmission of Cotton Leaf Curl Virus Vectored by Asia II-1 Genetic Group of Bemisia tabaci

Insects often coevolved with their mutualistic partners such as gut endosymbionts, which play a key in the physiology of host. Studies on such interactions between Bemisia tabaci and its primary and secondary endosymbionts have gained importance due to their indispensable roles in the biology of this insect. Present study reports the predominance of two secondary endosymbionts, Arsenophonus and Cardinium in the Asia II-1 genetic group of whitefly and elucidates their role in the transmission of its vectored Cotton leaf curl virus. Selective elimination of endosymbionts was optimized using serial concentration of ampicillin, chloramphenicol, kanamycin, tetracycline, and rifampicin administered to viruliferous whiteflies through sucrose diet. Primary endosymbiont, Portiera was unresponsive to all the antibiotics, however, rifampicin and tetracycline at 90 μg/ml selectively eliminated Arsenophonus from the whitefly. Elimination of Arsenophonus resulted in significant decrease in virus titer from viruliferous whitefly, further the CLCuV transmission efficiency of these whiteflies was significantly reduced compared to the control flies. Secondary endosymbiont, Cardinium could not be eliminated completely even with higher concentrations of antibiotics. Based on the findings, Arsenophonus plays a key role in the retention and transmission of CLCuV in the Asia II-1 genetic group of B. tabaci, while the role of Cardinium could not be established due to its unresponsiveness to antibiotics.

Copy number variation of two begomovirus acquired and inoculated by different cryptic species of whitefly, Bemisia tabaci in Okra

The whitefly, B.tabaci is a major pest of agricultural crops which transmits begomovirus in a species-specific manner. Yellow vein mosaic disease (YVMD) and okra leaf curl disease (OLCD) caused by distinct begomovirus are a major limitation to production of okra in India. In this framework the present investigation reports, for the first time, comparative study of begomovirus species viz. yellow vein mosaic virus (YVMV) and okra enation leaf curl virus (OELCuV) ingested and egested by two cryptic species (Asia I and Asia II 5) of B.tabaci at different time interval using detached leaf assay. A gradual increase of both virus copies were observed with increased feeding exposure in Asia I and Asia II 5. Both the genetic groups of whitefly could acquire the viruses within just 5 minutes of active feeding however, a significant amount of variation was noted in virus uptake by the both. At 24 hours of active feeding Asia II 5 acquired more of YVMV whereas, Asia I ingested more OELCuV. Similarly, the genetic group acquiring higher titre of virus egested higher amount during inoculation period. On the whole, it can be presumed that Asia I is a more effective transmitter of OELCuV whereas, Asia II 5 of YVMV further suggesting increased risk of virus pandemics (both YVMV and OELCuV) in regions where Asia I and Asia II 5 is dominant.

Dominance of Asia II 1 species of Bemisia tabaci in Pakistan and beyond

Globally, Whitefly (Bemisia tabaci) is one of the most important insect pests of crops that causes huge economical losses. The current study was designed to exclusively screen the B. tabaci species in the cotton field of Pakistan during 2017-2020 and have to conduct comparative analysis of B. tabaci species in Asia where Asia II 1 has been reported. A total of 5142 B. tabaci sequences of mitochondrial cytochrome oxidase 1 (mtCO1) from Asian countries were analyzed to determine the species and their distribution in the region. Our analysis over time and space showed that Asia II 1 has gradually dominated over Asia 1 in Punjab Province and over both Asia 1 and MEAM1 in Sindh Province. Asia has been divided into three regions i.e., South Asia (2524 sequences), Southeast Asia (757 sequences) and East Asia (1569 sequences) and dominance of different species of B. tabaci has been determined by calculating the relative percentage of each species. Interestingly, Asia II 1 has been found dominant in the neighboring region (northern zone) of India and also being dominant in its central zone. The dominance of Asia II 1 in Pakistan and northern India explains whitefly epidemic being reported in recent years.

Turning Waste into Beneficial Resource: Implication of Ageratum conyzoides L. in Sustainable Agriculture, Environment and Biopharma Sectors

The annual herb, Ageratum conyzoides L. (Asteraceae), is distributed throughout the world. Although invasive, it can be very useful as a source of essential oils, pharmaceuticals, biopesticides, and bioenergy. However, very limited information exists on the molecular basis of its different utility as previous investigations were mainly focused on phytochemical/biological activity profiling. Here we have explored various properties of A. conyzoides that may offer environmental, ecological, agricultural, and health benefits. As this aromatic plant harbors many important secondary metabolites that may have various implications, biotechnological interventions such as genomics, metabolomics and tissue-culture can be indispensable tools for their mass-production. Further, A. conyzoides acts as a natural reservoir of begomoviruses affecting a wide range of plant species. As the mechanisms of disease spreading and crop infection are not fully clear, whole-genome sequencing and various advanced molecular technologies including RNAi, CRISPER/Cas9, multi-omics approaches, etc., may aid to decipher the molecular mechanism of such disease development and thus, can be useful in crop protection. Overall, improved knowledge of A. conyzoides is not only essential for developing sustainable weed control strategy but can also offer potential ways for biomedicinal, environment, safe and clean agriculture applications.

Molecular, morphometric and digital automated identification of three Diaphorina species (Hemiptera: Liviidae)

Diaphorina is a species-rich genus, native to the tropics and subtropics of the Old World, particularly of more arid regions. One of the species, Diaphorina citri, is the economically most important pest of citrus. Diaphorina species are morphologically similar which makes their identification difficult. In this study, the accuracy of DNA barcoding, using mitochondrial cytochrome c oxidase subunit 1 (COI), geometric morphometrics of the forewing and digital image processing methods were tested for identification of the three Diaphorina species: D. chobauti, D. citri and D. zygophylli. Moreover, the published COI sequences of D. citri, D. communis and D. lycii obtained from Genbank were used for cluster analyses. DNA barcodes for D. chobauti and D. zygophylli are deposited in Genbank for the first time. The results of the molecular and geometric morphometric analyses are congruent and place D. chobauti as the sister taxon of the other Diaphorina species. The geometric morphometric analysis shows that in D. zygophylli the fore margin is slightly curved proximally and sharply bent distally, while in D. chobauti and D. citri it is straight proximally and weakly bent distally. The results of digital image processing show that the distribution of the dark pattern differs consistently in the three studied species.

Holocene population expansion of a tropical bee coincides with early human colonization of Fiji rather than climate change

There is substantial debate about the relative roles of climate change and human activities on biodiversity and species demographies over the Holocene. In some cases, these two factors can be resolved using fossil data, but for many taxa such data are not available. Inferring historical demographies of taxa has become common, but the methodologies are mostly recent and their shortcomings often unexplored. The bee genus Homalictus is developing into a tractable model system for understanding how native bee populations in tropical islands have responded to past climate change. We greatly expand on previous studies using sequences of the mitochondrial gene COI from 474 specimens and between 171 and 3928 autosomal (DArTSeq) single nucleotide polymorphism loci from 19 specimens of the native Fijian bee, Homalictus fijiensis, to explore its historical demography using coalescent and mismatch analyses. We ask whether past changes in demography were human- or climate-driven, while considering analytical assumptions. We show that inferred changes in population sizes are too recent to be explained by past climate change. Instead we find that a dramatic increase in population size for the main island of Viti Levu coincides with increasing occupation by humans and their modification of the environment. We found no corresponding change in bee population size for another major island, Kadavu, where human populations and agricultural activities have been historically very low. Our analyses indicate that molecular approaches can be used to disentangle the impacts of humans and climate change on a major tropical pollinator and that stringent analytical approaches are required for reliable interpretation of results.

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

BACKGROUND

Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes.

RESULTS

Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place.

CONCLUSIONS

Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

Impact of a novel Rickettsia symbiont on the life history and virus transmission capacity of its host whitefly (Bemisia tabaci)

Rickettsia consists of some of the most prevalent symbionts of insects and often plays a significant role in the biology of its hosts. Recently, a maternally inherited Torix group Rickettsia, provisionally named as RiTBt, was recorded in a species of notorious pest whitefly, tentatively named as Asia II 1, from the Bemisia tabaci complex. The role of this Rickettsia in the biology of its host is unknown. Here we investigated the impact of RiTBt on the performance and virus transmission capacity of Asia II 1. RiTBt did not significantly affect the life history parameters of the whitefly when the host insect was reared on tobacco, tomato, and cotton, three host plants with relatively low, medium and high suitability to the whitefly. Intriguingly, RiTBt slightly enhanced whitefly transmission of cotton leaf curl Multan virus (CLCuMuV), a virus that is transmitted by the whitefly in the field and has caused extensive damage to cotton production. Specifically, compared with whiteflies without RiTBt, following a 48 h virus acquisition whiteflies with RiTBt had higher titer of virus and showed higher efficiency of virus transmission. A rickettsial secretory protein BtR242 was identified as a putative virus-binding protein, and was observed to interact with the coat protein of CLCuMuV in vitro. Viral infection of the whitefly downregulated gene transcript levels of the BtR242 gene. These observations indicate that RiTBt has limited impact on the biology of the Asia II 1 whitefly, and whether this symbiont has functions in the biology of other host whiteflies warrants future investigation.

CAP Analysis of the Distribution of the Introduced Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex in Xinjiang, China and the Southerly Expansion of the Mediterranean Species

Bemisia tabaci (Gennadius) cryptic complex has invaded Xinjiang, China, since 1998. The distribution of Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) B. tabaci substrains has been gradually identified due to the development of molecular technology. In this study, the distribution of MED and MEAM1 in Xinjiang was determined by cleaved amplified polymorphic sequence (CAPs). Results showed that MED dominated in northern Xinjiang (84%), whereas MEAM1 was dominant in southern Xinjiang (72%). Five pairs of simple sequence repeat (SSR) primers were used to analyze the genetic diversity of B. tabaci among 36 geographic populations. The genetic diversity of MED and MEAM1was low and varied little among populations in Xinjiang (0.09 ± 0.14 and 0.09 ± 0.13, respectively). Based on ∆K statistic, 13 populations of MEAM1 could be classified into two subgroups at K = 2, whereas the 23 populations of MED could be classified into four subgroups at K = 4. However, Mantel t-test demonstrated no correlation between geographical and genetic distances among B. tabaci complex (R = 0.42, P = 1.00). Neighbor-joining and principal coordinate analysis showed that geographical isolation and interspecific differences were the main causes of the genetic variation. Gene flow predicted that MEAM1 was most likely introduced from Urumqi to the southern Xinjiang. Meanwhile, a large proportion of MED in Kashi region came from Changji and Yining. To block ongoing dispersal, strict detection and flower quarantine regulations need to be enforced.

Dominance of recombinant cotton leaf curl Multan-Rajasthan virus associated with cotton leaf curl disease outbreak in northwest India

Cotton leaf curl disease (CLCuD), caused by whitefly (Bemisiatabaci) transmitted single-stranded DNA viruses belonging to the Genus, Begomovirus (family, Geminiviridae) in association with satellite molecules; is responsible for major economic losses in cotton in three northwest (NW) Indian states Haryana, Punjab, and Rajasthan. Annual CLCuD incidences during 2012 to 2014 were estimated to be 37.5%, 63.6%, and 38.8% respectively. Cotton leaves were collected from symptomatic plants annually for three years and subjected to DNA isolation, followed by rolling circle amplification (RCA), cloning, and DNA sequencing of apparently full-length begomoviral genomes and associated betasatellites and alphasatellites. Among the thirteen CLCuD-begomoviral genomes recovered, eight were identified as Cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Ra), one as -Pakistan (PK) and another as -Faisalabad (Fai), whereas, three were as Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu), indicating that CLCuMuV-Ra was the most prevalent begomovirus species. Five of the eight CLCuMuV-Ra sequences were found to be recombinants. The CLCuMuV-Ra- associated satellites consisted of Cotton leaf curl Multan betasatellite (CLCuMB), and Gossypium darwinii symptomless alphasatellite (GDarSLA), and Croton yellow vein mosaic alphasatellite (CrYVMoA). The second most abundant helper virus species, CLCuKoV-Bu, was associated with CLCuMB and GDarSLA.

Molecular and morphometric identification of pistachio psyllids with niche modeling of Agonoscena pistaciae (Hemiptera: Aphalaridae)

Species of Agonoscena (Hemiptera: Aphalaridae) are key pests of pistachio in all of the most important pistachio producing countries in the Old World. The efficiency and accuracy of DNA barcoding for the identification of Agonoscena species were tested using mitochondrial cytochrome c oxidase subunit 1 (mtCO1) and cytochrome b (cytb) gene sequences. Moreover, morphometric sexual dimorphism was studied. Finally, the potential geographical distribution of Agonoscena pistaciae, the most important pistachio pest, was calculated using the MaxEnt model. Similar relationships of clustering were found in the morphometric analysis and the molecular analyses with mtCO1 and cytb genes, with A. bimaculata and A. pistaciae being closely related, and A. pegani constituting their sister group. Although the results showed that the cytb gene is a better marker for barcoding in this group, the mtCO1 gene clearly separates the three psyllid species making mtCO1 suitable for diagnostic purposes. A geometric morphometric analysis showed that the distance between landmark number 7 (bifurcation of vein M) to the fore margin of the forewing, and the distance between landmarks number 6 (apex of vein Cu1b) and 11 (wing base), are the most important geometric characters for diagnosing the studied species. Moreover, the forewing shape of males vs females is similar in A. pistaciae and A. bimaculata but differs significantly in A. pegani. In the ecological niche modeling of the distribution of A. pistaciae, the most important contribution was made by the variable 'minimum temperature of coldest period'. The most suitable areas for A. pistaciae are restricted to Eastern, Southern and some parts of Central Iran.

Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II-Bemisia tabaci mitotypes in Pakistan

Endosymbionts associated with the whitefly Bemisia tabaci cryptic species are known to contribute to host fitness and environmental adaptation. The genetic diversity and population complexity were investigated for endosymbiont communities of B. tabaci occupying different micro-environments in Pakistan. Mitotypes of B. tabaci were identified by comparative sequence analysis of the mitochondria cytochrome oxidase I (mtCOI) gene sequence. Whitefly mitotypes belonged to the Asia II-1, -5, and -7 mitotypes of the Asia II major clade. The whitefly-endosymbiont communities were characterized based on 16S ribosomal RNA operational taxonomic unit (OTU) assignments, resulting in 43 OTUs. Most of the OTUs occurred in the Asia II-1 and II-7 mitotypes (r 2 = .9, p < .005), while the Asia II-5 microbiome was less complex. The microbiome OTU groups were mitotype-specific, clustering with a basis in phylogeographical distribution and the corresponding ecological niche of their whitefly host, suggesting mitotype-microbiome co-adaptation. The primary endosymbiont Portiera was represented by a single, highly homologous OTU (0%-0.67% divergence). Two of six Arsenophonus OTUs were uniquely associated with Asia II-5 and -7, and one occurred exclusively in Asia II-1, two only in Asia II-5, and one in both Asia II-1 and -7. Four other secondary endosymbionts, Cardinium, Hemipteriphilus, Rickettsia, and Wolbachia OTUs, were found at ≤29% frequencies. The most prevalent Arsenophonus OTU was found in all three Asia II mitotypes (55% frequency), whereas the same strain of Cardinium and Wolbachia was found in both Asia II-1 and -5, and a single Hemipteriphilus OTU occurred in Asia II-1 and -7. This pattern is indicative of horizontal transfer, suggestive of a proximity between mitotypes sufficient for gene flow at overlapping mitotype ecological niches.

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

Transmission efficiency of Cotton leaf curl Multan virus by three cryptic species of Bemisia tabaci complex in cotton cultivars

Cotton leaf curl Multan virus (CLCuMuV) is a serious and economically important viral disease agent in cotton and ornamental plants like Hibiscus in many regions of the world, especially in South Asia. CLCuMuV is transmitted exclusively by Bemisia tabaci cryptic species complex. This virus was recently recorded in southern China, presumably an invasion from South Asia. This study was performed to estimate the efficiency of three species of the B. tabaci whitefly complex (tentatively named as MEAM1, MED and Asia II 7, respectively) to transmit CLCuMuV and Cotton leaf curl multan virus betasatelite (CLCuMuB). Transmission assays and real-time quantitative PCR were conducted using three cultivars of cotton, Gossypium hirsutum, including 112-2, Xinhai-21 and Zhongmian-40. The results indicated that Asia II 7 was able to transmit the virus to two of the cotton cultivars, i.e. 112-2 and Xinhai-21, with the highest transmission efficiencies of 40% and 30%, respectively, but was unable to transmit the virus to the cotton cultivar Zhongmian-40. MEAM1 and MED failed to transmit CLCuMuV and CLCuMuB to any of the three cotton cultivars. After the three cryptic species of whiteflies had fed on virus-infected cotton plants for 48 h, the relative quantity of CLCuMuV in Asia II 7 was detected to be significantly higher than that in both MEAM1 and MED (P < 0.05). These results indicate that among the three species of whiteflies Asia II 7 is likely the most efficient vector for CLCuMuV and CLCuMuB in Malvaceae crops in China. Our findings provide valuable information to the control of viral diseases caused by CLCuMuV in the field.

The impact of one-decade ecological disturbance on genetic changes: a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran

Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake’s native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (∼300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na⁺/K⁺ ATPase. There was no notable difference in genetic variation detected for COI and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na⁺/K⁺ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana.

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.

Genetic Diversity of Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex Across Malaysia

The tobacco whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex with members capable of inducing huge economic losses. Precise identification of members of this complex proves essential in managing existing populations and preventing new incursions. Despite records of serious outbreaks of this pest in Malaysia little is known about species status of B. tabaci in this region. To address this, a comprehensive sampling of B. tabaci from different host plants was conducted in 10 states of Malaysia from 2010 to 2012. Members of the complex were identified by sequencing partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene and constructing a Bayesian phylogenetic tree. Seven putative species were identified including Asia I, Mediterranean (MED), China 1, China 2, Asia II 6, Asia II 7, and Asia II 10. The most important finding of the study is the identification of the invasive MED species from locations without previous records of this species. All putative species except Asia I and MED are recorded from Malaysia for the first time. This study provided the first introductory map of B. tabaci species composition in Malaysia and emphasizes the urgent need for further studies to assess the status of MED invasion in this country.

Cotton Leaf Curl Disease: Which Whitefly Is the Vector?

Cotton leaf curl disease is one of the most significant constraints to the production of cotton. In the past decades our understanding of the begomoviruses (family Geminiviridae) causing the disease has improved, but little is known regarding transmission of these viruses by the different species of whiteflies in the Bemisia tabaci complex. We compared transmission efficiency of cotton leaf curl Multan virus (CLCuMuV), one of the major begomoviruses associated with cotton leaf curl disease, by four whitefly species, of which two are indigenous to Asia and two are invasive worldwide. Only the indigenous Asia II 1 species was able to transmit this virus with high efficiency. By quantifying the virus and using immunoflorescence assays, we found that the differential transmission was associated with the varying efficiency of CLCuMuV to cross the midgut of various whitefly species. Further, we verified the role of coat protein in the whitefly transmission of CLCuMuV. Based on a phylogenetic analysis of the virus coat proteins, we found that most begomoviruses associated with cotton leaf curl disease might share similar whitefly transmission characteristics. These findings advance our understanding of the nature of cotton leaf curl disease and provide information for the development of control and preventive strategies against this disease.

Bemisia tabaci-mediated facilitation in diversity of begomoviruses: Evidence from recent molecular studies

Begomoviruses are considered as one of the most notorious plant viruses worldwide, which cause substantial economic losses to various field crops. Management of begomoviruses has become a challenge due to the continuous evolution and the emergence of new strains. Bemisia tabaci is globally known to be the key vector of begomoviruses, having relatively high reproductivity, fast dispersal ability, high survival rate due to its polyphagous nature and high resistance to various groups of insecticides. Continuous transmission of begomoviruses by the vector has led to the development and spread of epidemics of various diseases worldwide. In this review, we have critically analyzed the various dynamics which facilitate the diversity of begomoviruses through their vector. The interaction of begomovirus-whitefly leads to continuous research activities regarding management of both virus and its vector, thus opening exciting new horizons to formulate potential control strategies to ensure a disease-free cropping environment.

DNA barcoding of five Japanese encephalitis mosquito vectors (Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui)

Culex mosquitoes can act as vectors of several important diseases, including Japanese encephalitis, West Nile virus, St. Louis encephalitis and equine encephalitis. Besides the neurological sequelae caused in humans, Japanese encephalitis can lead to abortion in sows and encephalitis in horses. Effective vector control and early diagnosis, along with continuous serosurveillance in animals, are crucial to fight this arboviral disease. However, the success of vector control operations is linked with the fast and reliable identification of targeted species, and knowledge about their biology and ecology. Since the DNA barcoding of Culex vectors of Japanese encephalitis is scarcely explored, here we evaluated the efficacy of this tool to identify and analyze the variations among five overlooked Culex vectors of Japanese encephalitis, Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui, relying to the analysis of mitochondrial CO1 gene. Variations in their base pair range were elucidated by the entropy H_x plot. The differences among individual conspecifics and on base pair range across the same were studied. The C (501-750 bp) region showed a moderate variation among all the selected species. C. tritaeniorhynchus exhibited the highest variation in all the ranges. The observed genetic divergence was partially non-discriminatory. i.e., the overall intra- and inter nucleotide divergence was 0.0920 (0.92%) and 0.125 (1.25%), respectively. However, 10X rule fits accurately intraspecies divergence <3% for the five selected Culex species. The analysis of individual scatter plots showed threshold values (10X) of 0.008 (0.08%), 0.005 (0.05%), 0.123 (1.23%), 0.033 (0.33%) and 0.019 (0.19%) for C. fuscocephala, C. gelidus, C. tritaeniorhynchus, C. pseudovishnui and C. vishnui, respectively. The C. tritaeniorhynchus haplotypes KU497604, KU497603, AB690847 and AB690854 exhibited the highest divergence range, i.e., from 0.465 -0.546. Comparatively, the intra-divergence among the other haplotypes of C. tritaeniorhynchus ranged from 0-0.056. The maximum parsimony tree was formed by distinctive conspecific clusters with appreciable branch values illustrating their close congruence and extensive genetic deviations. Overall, this study adds valuable knowledge to the molecular biology and systematics of five overlooked mosquito species acting as major vectors of Japanese encephalitis in Asian countries.

Cryptic Plutella species show deep divergence despite the capacity to hybridize

Background

Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world’s most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays.

Results

The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of P. xylostella.

Conclusions

Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1183-4) contains supplementary material, which is available to authorized users.

Genetic diversity of begomoviruses in Pakistan captured through a vector based survey

Begomoviruses (Geminiviridea), transmitted by whiteflies, constitute one of the most dangerous groups of plant viruses posing a severe threat to economically important crops in tropical and sub-tropical areas. In this study, whiteflies were collected from various locations all over Pakistan. The begomoviruses carried by these whiteflies were detected by PCR with the degenerative primers pair AV94/Dep3. Analysis of the 177 sequences obtained in our study, revealed 14 distinct begomovirus species, including five which were not previously reported in this country. Putative novel strains of Corchorus yellow vein virus (CoYVV) and Chilli leaf curl virus (ChiLCV) showing less than 90% identity with the previously available taxa were also identified. The greatest number of begomoviruses per single site was detected in Sindh province, where up to five different begomovirus species were identified from the same cropping field. Moreover, Cotton leaf curl Multan virus - Rajasthan (CLCuMuV-Ra) was found prevalent in all the cotton growing areas. The data reported here may be useful in the development of control measures against begomoviruses.

Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly)

Trialeurodes vaporariorum (Westwood, 1856) (Greenhouse whitefly) is an agricultural pest of global importance. It is associated with damage to plants during feeding and subsequent virus transmission. Yet, global phylogenetic relationships, population structure, and estimation of the rates of gene flow within this whitefly species remain largely unexplored. In this study, we obtained and filtered 227 GenBank records of mitochondrial cytochrome c oxidase I (mtCOI) sequences of T. vaporariorum, across various global locations to obtain a final set of 217 GenBank records. We further amplified and sequenced a ~750 bp fragment of mtCOI from an additional 31 samples collected from Kenya in 2014. Based on a total of 248 mtCOI sequences, we identified 16 haplotypes, with extensive overlap across all countries. Population structure analysis did not suggest population differentiation. Phylogenetic analysis indicated the 2014 Kenyan collection of samples clustered with a single sequence from the Netherlands to form a well-supported clade (denoted clade 1a) nested within the total set of sequences (denoted clade 1). Pairwise distances between sequences show greater sequence divergence between clades than within clades. In addition, analysis using migrate-n gave evidence for recent gene flow between the two groups. Overall, we find that T. vaporariorum forms a single large group, with evidence of further diversification consisting primarily of Kenyan sequences and one sequence from the Netherlands forming a well-supported clade.

Genetic diversity of Leishmania donovani that causes cutaneous leishmaniasis in Sri Lanka: a cross sectional study with regional comparisons

BACKGROUND

Leishmania donovani is the etiological agent of visceral leishmaniasis (VL) in the Indian subcontinent. However, it is also known to cause cutaneous leishmaniasis (CL) in Sri Lanka. Sri Lankan L. donovani differs from other L. donovani strains, both at the molecular and biochemical level. To investigate the different species or strain-specific differences of L. donovani in Sri Lanka we evaluated sequence variation of the kinetoplastid DNA (kDNA).

METHODS

Parasites isolated from skin lesions of 34 CL patients and bone marrow aspirates from 4 VL patients were genotyped using the kDNA minicircle PCR analysis. A total of 301 minicircle sequences that included sequences from Sri Lanka, India, Nepal and six reference species of Leishmania were analyzed.

RESULTS

Haplotype diversity of Sri Lankan isolates were high (H d  = 0.757) with strong inter-geographical genetic differentiation (F ST  > 0.25). In this study, L. donovani isolates clustered according to their geographic origin, while Sri Lankan isolates formed a separate cluster and were clearly distinct from other Leishmania species. Within the Sri Lankan group, there were three distinct sub-clusters formed, from CL patients who responded to standard antimony therapy, CL patients who responded poorly to antimony therapy and from VL patients. There was no specific clustering of sequences based on geographical origin within Sri Lanka.

CONCLUSION

This study reveals high levels of haplotype diversity of L. donovani in Sri Lanka with a distinct genetic association with clinically relevant phenotypic characteristics. The use of genetic tools to identify clinically relevant features of Leishmania parasites has important therapeutic implications for leishmaniasis.

Diversity and Distribution of Cryptic Species of the Bemisia tabaci (Hemiptera: Aleyrodidae) complex in Pakistan

Bemisia tabaci (Gennadius; Hempitera: Aleyrodidae) is considered to be a cryptic (sibling) species complex, the members of which exhibit morphological invariability while being genetically and behaviorally distinct. Members of the complex are agricultural pests that cause direct damage by feeding on plants, and indirectly by transmitting viruses that cause diseases leading to reduced crop yield and quality. In Pakistan, cotton leaf curl disease, caused by multiple begomovirus species, is the most economically important viral disease of cotton. In the study outlined here, the diversity and geographic distribution of B. tabaci cryptic species was investigated by analyzing a taxonomically informative fragment of the mitochondrial cytochrome c oxidase 1 gene (mtCOI-3'). The mtCOI-3' sequence was determined for 285 adult whiteflies and found to represent six cryptic species, the most numerous being Asia II-1 and Middle East Asia Minor 1 (MEAM-1), the later also referred to as the B-biotype, which was previously thought to be confined to Sindh province but herein, was also found to be present in the Punjab province. The endemic Asia I was restricted to Sindh province, while an individual in the Asia II-8 was identified in Pakistan for the first time. Also for the first time, samples were collected from northwestern Pakistan and Asia II-1 was identified. Results indicate that in Pakistan the overall diversity of B. tabaci cryptic species is high and, based on comparisons with findings from previous studies, the distribution is dynamic.

Genetic diversity of Bemisia tabaci species colonizing cassava in Central African Republic characterized by analysis of cytochrome c oxidase subunit I

After 2007, upsurges of whiteflies on cassava plants and high incidences of cassava diseases were observed in Central African Republic. This recent upsurge in the abundance of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) was directly linked to serious damage to cassava crops resulting from spread of whitefly-borne cassava mosaic geminiviruses (CMGs). There is currently very little information describing whitefly populations on cassava and associated crops in Central African Republic. The current study aimed to address this gap, and to determine whether the increasing damage associated with B. tabaci whiteflies was the consequence of a new invasion, or an upsurge of a local population. The molecular genetic identification and phylogenetic relationships of 898 B. tabaci adult individuals collected from representative locations (54) throughout CAR were determined based on their mitochondrial cytochrome oxidase I sequences (mtCOI). Field and ecological data were also collected from each site, including whitefly abundance, CMD incidence, host plants colonized by B. tabaci and agro-ecological zone. Phylogenetic analysis of the whitefly mtCOI sequences indicated that SSA1 (-SG1, -SG2), SSA3, MED, MEAM1 and Indian Ocean (IO) putative species occur in CAR. One specific haplotype of SSA1-SG1 (SSA1-SG1-P18F5) predominated on most cassava plants and at the majority of sites. This haplotype was identical to the SSA1-SG1 Mukono8-4 (KM377961) haplotype that was recorded from Uganda but that also occurs widely in CMD pandemic-affected areas of East Africa. These results suggest that the SSA1-SG1-P18F5 haplotype occurring in CAR represents a recent invasive population, and that it is the likely cause of the increased spread and severity of CMD in CAR. Furthermore, the high mtDNA sequence diversity observed for SSA1 and its broad presence on all sites and host plants sampled suggest that this genetic group was the dominant resident species even before the arrival of this new invasive haplotype.

Genetics and Genomics of Cotton Leaf Curl Disease, Its Viral Causal Agents and Whitefly Vector: A Way Forward to Sustain Cotton Fiber Security

Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc., and practicing mixed type farming system have further exaggerated the situation by adding synergy to the evolution of new viral strains and vectors. Efforts to control this disease using host plant resistance remained successful using two gene based-resistance that was broken by the evolution of new resistance breaking strain called Burewala virus. Development of transgenic cotton using both pathogen and non-pathogenic derived approaches are in progress. In future, screening for new forms of host resistance, use of DNA markers for the rapid incorporation of resistance into adapted cultivars overlaid with transgenics and using genome editing by CRISPR/Cas system would be instrumental in adding multiple layers of defense to control the disease-thus cotton fiber production will be sustained.

RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants

The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses to crop and ornamental plants worldwide. Using RNA interference (RNAi) to down regulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus disease spread. Using a Tobacco rattle virus-derived plasmid for in planta transient expression of double stranded RNA (dsRNA) homologous to the acetylcholinesterase (AChE) and ecdysone receptor (EcR) genes of B. tabaci, resulted in significant adult whitefly mortality. Nicotiana tabacum L. plants expressing dsRNA homologous to B. tabaci AChE and EcR were constructed by fusing sequences derived from both genes. Mortality of adult whiteflies exposed to dsRNA by feeding on N. tabacum plants, compared to non-dsRNA expressing plants, recorded at 24-hr intervals post-ingestion for three days, was >90% and 10%, respectively. Analysis of gene expression by real time quantitative PCR indicated that whitefly mortality was attributable to the down-regulation of both target genes by RNAi. Results indicated that knock down of whitefly genes involved in neuronal transmission and transcriptional activation of developmental genes, has potential as a bio-pesticide to reduce whitefly population size and thereby decrease virus spread.

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.

Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCuKoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10^-4) and CLCuKoV-CP gene (2.706X10^-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.

DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes

Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5ʹ (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

Comparison of transmission of Papaya leaf curl China virus among four cryptic species of the whitefly Bemisia tabaci complex

Begomoviruses are transmitted by cryptic species of the whitefly Bemisia tabaci complex, often in a species-specific manner. Papaya leaf curl China virus (PaLCuCNV) has been recorded to infect several crops including papaya, tomato and tobacco in China. To help assess the risks of spread of this virus, we compared the acquisition, retention and transmission of PaLCuCNV among four species of whiteflies, Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED), Asia 1 and Asia II 7. All four species of whiteflies are able to acquire, retain and transmit the virus, but with different levels of efficiency. Transmission tests using tomato as the host plant showed that MEAM1 transmitted PaLCuCNV with substantially higher efficiency than did MED, Asia 1 and Asia II 7. Furthermore, accumulation of PaLCuCNV in the whiteflies was positively associated with its efficiency of transmitting the virus. Altogether, these findings indicate that MEAM1 is the most efficient vector for PaLCuCNV in the four species of whiteflies, and suggest that risks of PaLCuCNV pandemics are high in regions where MEAM1 occurs.