The predatory mite Pronematus ubiquitus curbs Aculops lycopersici damage under greenhouse conditions.

BACKGROUND: The tomato russet mite, Aculops lycopersici, is a major worldwide pest infesting tomato crops for which only few control methods are available. At present, no commercialized beneficial organism has proven to be an effective biological control agent of the pest. As there is a strong need to develop alternatives to synthetic insecticides, we assessed the efficacy of an iolinid mite, Pronematus ubiquitus, as a preventive method against A. lycopersici in comparison with a curative treatment in a replicated experiment in the greenhouse. RESULTS: After pre-establishment of P. ubiquitus supplied with cattail pollen, followed by infestation of A. lycopersici, the predator was able to reduce pest populations by 98% as compared with control plants. Probably due to lack of food and high temperature, the number of P. ubiquitus decreased during the season and so the Eriophyid population rose, along with crop damage. The sulphur treatment could stop the progress of A. lycopersici, but their population levels remained high. CONCLUSION: Pronematus ubiquitus has great potential to prevent the establishment of the tomato russet mite. Even if a curative treatment affects the pest mite, the use of a preventive method is preferable as such insecticides/acaricides are harmful for beneficials and are applied after symptom appearance, when the pest pressure is already high. Despite the need to optimise management of the predator throughout the season, P. ubiquitus proved to be able to establish successfully on tomato plants. © 2023 Society of Chemical Industry.

Impact of cooking on the protein quality of Russet potatoes.

Despite being low in crude protein, on a fresh weight basis, given their overall contribution to the North American diet, potatoes contribute approximately 2%-4% of the population's protein intake. However, the quality of the protein remains ill-defined. To that end, Russet potatoes were secured and subjected to various cooking conditions (raw [control], boiled, baked, microwaved, and fried [3, 6, and 9 min]) to determine the impact of cooking method on protein quality, as determined by amino acid score (AAS) and indices of in vivo true fecal protein digestibility (TFPD%; rodent bioassay) and in vitro protein digestibility (pH-drop, pH-Stat, and simulated gastrointestinal digestion both static and dynamic). The AAS of raw Russet potatoes was 0.67 ± 0.01, with histidine being the limiting AA. Frying led to a significant reduction in the AAS, however, other cooking methods yielded similar results to the raw control. The TFPD% of raw potato was low (40.5% ± 3.9%) and was significantly enhanced to over 80% with all cooking methods. Similar patterns were observed with all in vitro measures, however, all methods yielded higher values for the raw control samples. Final protein digestibility-corrected AAS (PDCAAS; product of AAS and TFPD%) values ranged from 0.27 (raw) to a high of 0.57 (boiled), with cooked values being comparable to other plant-based protein sources, including grains, and some nuts and pulses. In vitro PDCAAS values followed similar trends. This study defined the protein quality of cooked Russet potatoes and provides data for use in defining the quality of total protein consumed in the North American diet.

Modelling the interaction between a pest (Aculops lycopersici), two predators (Pronematus ubiquitus and Macrolophus pygmaeus) and climate variables: a 3-year greenhouse study in a tomato crop.

BACKGROUND: The tomato russet mite, Aculops lycopersici, is a major pest in tomato crops, causing damage through leaf and stem browning, defoliation and russeting of fruit. Biological control of this mite on tomato plants is difficult. While several phytoseiid mites feed on the pest, they cannot survive, move, or reproduce on tomato plants due to the presence of glandular trichomes. Pronematus ubiquitus has recently been identified as a biocontrol agent of A. lycopersici in tomato crops, but the predator-prey interaction between these two species is not well studied. In this paper, we present a validated logistic regression predator-prey model based on a 3-year study supplemented with additional datasets. Besides the predator and the prey, this model takes into account an extra generalist predator, Macrolophus pygmaeus, and various climate parameters. RESULTS: The population trend of A. lycopersici is best explained by the presence of the predator P. ubiquitus, the relative humidity and the fact that the crop was lit or unlit using artificial light. P. ubiquitus has proved to be an efficient biocontrol agent of A. lycopersici. For P. ubiquitus the presence of M. pygmaeus, the vapour pressure deficit, the number of light hours and radiation explained the population trend best. For both the predator and the prey density-dependent interactions were identified. Model outcomes are discussed in detail. CONCLUSION: Our study provides insights into the potential use of P. ubiquitus as a biocontrol agent for A. lycopersici in tomato crops in combination with M. pygmaeus. However, we highlight the importance of considering the presence of other predators and environmental conditions when developing integrated pest management strategies. © 2023 Society of Chemical Industry.

Comprehensive analysis of KCS gene family in pear reveals the involvement of PbrKCSs in cuticular wax and suberin synthesis and pear fruit skin formation.

Cuticular wax, cutin and suberin polyesters covering the surface of some fleshy fruit are tightly associated with skin color and appearance. ß-Ketoacyl-CoA synthase (KCS) is a rate-limiting enzyme participating in the synthesis of very-long-chain fatty acids (VLCFAs), the essential precursors of cuticular waxes and aliphatic monomers of suberin. However, information on the KCS gene family in pear genome and the specific members involved in pear fruit skin formation remain unclear. In the present study, we performed an investigation of the composition and amount of cuticular waxes, cutin and aliphatic suberin in skins of four sand pear varieties with distinct colors (russet, semi-russet, and green) and demonstrated that the metabolic shifts of cuticular waxes and suberin leading to the significant differences of sand pear skin color. A genome-wide identification of KCS genes from the pear genome was conducted and 35 KCS coding genes were characterized and analyzed. Expression profile analysis revealed that the KCS genes had diverse expression patterns among different pear skins and the transcript abundance of PbrKCS15, PbrKCS19, PbrKCS24, and PbrKCS28 were consistent with the accumulation of cuticular waxes and suberin in fruit skin respectively. Subcellular localization analysis demonstrated that PbrKCS15, PbrKCS19, PbrKCS24 and PbrKCS28 located on the endoplasmic reticulum (ER). Further, transient over-expression of PbrKCS15, PbrKCS19, and PbrKCS24 in pear fruit skins significantly increased cuticular wax accumulation, whereas PbrKCS28 notably induced suberin deposition. In conclusion, pear fruit skin color and appearance are controlled in a coordinated way by the deposition of the cuticular waxes and suberin. PbrKCS15, PbrKCS19, and PbrKCS24 are involved in cuticular wax biosynthesis, and PbrKCS28 is involved in suberin biosynthesis, which play essential roles in pear fruit skin formation. Moreover, this work provides a foundation for further understanding the functions of KCS genes in pear.

Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time.

Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.

Identification of nsLTP family in Chinese white pear (Pyrus bretschneideri) reveals its potential roles in russet skin formation.

MAIN CONCLUSION: Identification of PbLTP genes in pear and functional characterization of PbLTP4 in the transport of suberin monomers of russet skin formation. Non-specific lipid-transfer protein (nsLTP) is an abundant and diverse alkaline small molecule protein in the plant kingdom with complex and diverse biophysiological functions, such as transfer of phospholipids, reproductive development, pathogen defence and abiotic stress response. Up to now, only a tiny fraction of nsLTPs have been functionally identified, and the distribution of nsLTPs in pear (Pyrus bretschneideri) (PbLTPs) has not been fully characterized. In this study, the genome-wide analysis of the nsLTP gene family in the pear genome identified 67 PbLTP proteins, which could be divided into six types (1, 2, C, D, E, and G). Similar intron/exon structural patterns were observed in the same type, strongly supporting their close evolutionary relationship. In addition, PbLTP4 was highly expressed in russet pear skin compared with green skin, which was located in the plasma membrane. Coexpression network analysis showed that PbLTP4 closely related to suberin biosynthetic genes. The biological function of PbLTP4 in promoting suberification has been demonstrated by overexpression in Arabidopsis. Identification of suberin monomers showed that PbLTP4 promotes suberification by regulating 9,12-octadecadienoic acid and hexadecanoic acid transport. These results provide helpful insights into the characteristics of PbLTP genes and their biological function in the transport of suberin monomers of russet skin formation.

A Novel Approach to Tally Aculops cannabicola (Acari: Eriophyidae) for Field and Laboratory Studies.

The hemp russet mite, Aculops cannabicola (Farkas) is a key pest of hemp (Cannabis sativa L.). Given its microscopic size, estimating the size of its populations can be a major limitation to control this pest. Here, we describe a method to count A. cannabicola using photographs taken with a handheld digital microscope. We compared the consistency and strength of the relationship between photographic- and microscope-based counts of mites from infested plants. Among the three sections of the leaflet, the maximum consistency levels were observed in the proximal (50%) and middle photographs (50%). However, it reached from 64% to 100% when the three sections were considered. Photographic and a microscope-based counts were positively correlated (>0.7). A single photograph can be a good predictor of the total mites per leaflet, however, using two pictures (proximal and middle sections) will increase the consistency of the abundance of A. cannabicola per leaflet. A minimum of 22 leaflets per sampling event can support a strong correlation between the microscope and photographic counts. Our method requires low budget and training and takes short time (0.4 to 1.3 min per leaflet) to count mites per sample. Additionally, photographs can be stored on a smartphone, computer, or tablet, allowing users to share, store and process the photos. This method simplifies counts of A. cannabicola on hemp for research purposes and provides a practical tool for growers to assess mite populations for management decisions. In addition, it may be useful for monitoring eriophyid mites on cultivated plants.

Control of Aculops lycopersici with the Predatory Mite Transeius montdorensis.

In this study, the predatory mite Transeius montdorensis (Acari, Phytoseiidae) was tested for the control of the tomato russet mite (TRM) Aculops lycopersici (Acari, Eriophyidae) in experiments with small plants, under semi-field and crop conditions. The releasing strategy consisted of repeatedly introducing the predator together with additional breeding prey. The predator was able to move and disperse to the upper part of the tomato plant where the TRM seeks refuge. At the crop level, significant reductions in TRM populations were observed that resulted in a significantly higher yield compared to the conventional control plot, where pesticides were used to control the pest. Caution should be taken when extreme temperatures or humidity occur as they could be deleterious to the predator population. Hence, crop practices should include the management of environmental parameters in the greenhouse to ensure the success of this TRM-control strategy. In conclusion, this biological approach seems to be an effective measure to control the pest and should be further implemented at crop level.

The role of a synanthropic bird in the nest niche expansion of a secondary cavity nester to man-made structures.

Species with similar ecological characters often compete with each other; however, a species may also facilitate the survival or reproduction of another ecologically similar species, although such interaction is rarely documented in birds. Here, we reported a facilitative species interaction between Asian house martins (Delichon dasypus) and russet sparrows (Passer cinnamomeus), both passerines using closed nests, in a montane farming area of Taiwan. We found that Asian house martins constructed dome-shaped nests in human houses that provided additional nest sites for russet sparrows, secondary cavity nesters with greatly declining populations in Taiwan. Russet sparrows that used house martin nests had reproductive success comparable to those that used artificial nest boxes. However, Asian house martins avoided reclaiming sparrow-used nests, which reduced their available nest sites. Interestingly, our results imply that man-made structures may be used as a conservation tool to improve the breeding of the endangered russet sparrows via this facilitative interaction.

MYB1R1 and MYC2 Regulate ω-3 Fatty Acid Desaturase Involved in ABA-Mediated Suberization in the Russet Skin of a Mutant of 'Dangshansuli' (Pyrus bretschneideri Rehd.).

Russeting, a disorder of pear fruit skin, is mainly caused by suberin accumulation on the inner part of the outer epidermal cell layers. ABA was identified as a crucial phytohormone in suberification. Here, we demonstrated that the ABA content in russet pear skin was higher than in green skin. Then, ABA was applied to explore the changes in phenotype and suberin composition coupled with RNA-Seq and metabolomics to investigate the probably regulatory pathway of ABA-mediated suberification. The results showed that ABA treatment increased the expression of ω-3 fatty acid desaturase (FAD) and the content of α-linolenic acid. We identified 17 PbFADs in white pear, and the expression of PbFAD3a was induced by ABA. In addition, the role of PbFAD3a in promoting suberification has been demonstrated by overexpression in Arabidopsis and VIGS assays in the fruitlets. GUS staining indicated that the promoter of PbFAD3a was activated by ABA. Furthermore, MYC2 and MYB1R1 have been shown to bind to the PbFAD3a promoter directly and this was induced by ABA via yeast one-hybrid (Y1H) screening and qRT-PCR. In summary, our study found that ABA induces the expression of MYC2 and MYB1R1 and activates the PbFAD3a promoter, contributing to the formation of russet pear skin. Functional identification of key transcription factors will be the goal of future research. These findings reveal the molecular mechanism of ABA-mediated suberization in the russet skin and provide a good foundation for future studies on the formation of russet skin.

Dual protection: A tydeoid mite effectively controls both a problem pest and a key pathogen in tomato.

BACKGROUND: The tomato russet mite (TRM), Aculops lycopersici, and powdery mildew (PM), Oidium neolycopersici, are two major problems in tomato cultivation for which no effective biocontrol solutions exist to date. In a greenhouse compartment, we investigated the potential of preventatively establishing the iolinid omnivorous mite Pronematus ubiquitus on potted tomato plants to control both pest and pathogen simultaneously. RESULTS: Using Typha pollen, P. ubiquitus established well on tomato plants, with numbers reaching up to 250 motiles per tomato leaflet. The built-up population was capable of controlling subsequent infestations with both TRM and PM. This represents the first report of an arthropod protecting a crop against pests as well as disease. CONCLUSION: The implementation of P. ubiquitus in tomato crops could be a real game-changer as it eliminates the need for repeated pesticide use or sulphur applications. The finding that arthropods can effectively control diseases opens up new opportunities for biological crop protection. © 2021 Society of Chemical Industry.

Density thresholds and the incorporation of biocontrol into decision-making to enhance the control of Cacopsylla pyri in pear (cv. Ercolini) orchards.

BACKGROUND: Economic injury level (EIL) and economic threshold (ET) are customary tools for integrated pest management. Cacopsylla pyri L. is a major pest in pear orchards. The aim of this work was to establish EIL and ET for the optimization of the use of insecticides to control this psyllid, considering biocontrol and two spraying strategies (low-toxicity versus broad spectrum chemicals). This research was conducted over 4 years in five commercial pear, cv. Ercolini, orchards in south-eastern Spain. RESULTS: Psyllids and ant populations were followed using periodic sampling, and the russet on fruits was quantified. The effect of spray intensity and ant exclusion on psyllid abundance and yield were also tested: both had a significant effect on the cumulative number of C. pyri (CNP), yield and fruit weight. Yield was found to be negatively correlated with CNP. The russet index (RI) increased in a sigmoidal fashion as a function of CNP, being significantly higher with than without ant exclusion. The commercial categorization of fruits was explained satisfactorily as a function of CNP and the cumulative number of ants (CNA). The quantitative EIL was established at a CNP of 427.2 for spraying with paraffinic oil and 425.7 for abamectin. As for the cosmetic EIL, when CNA was zero, this EIL was 24.2, at a CNP of 16.6 for spraying with paraffinic oil or abamectin. CONCLUSIONS: The use of products of low toxicity, for the conservation of ants, is expected to increase ET and, thus, reduce the intensity of spraying. © 2021 Society of Chemical Industry.

Enhanced top-down control of herbivore population growth on plants with impaired defences.

Herbivore densities can be regulated by bottom-up and top-down forces such as plant defences and natural enemies, respectively. These forces can interact with each other to increase plant protection against herbivores; however, how much complementarity exists between bottom-up and top-down forces still remains to be fully elucidated. Particularly, because plant defences can hinder natural enemies, how these interactions affect herbivore performance and dynamics remains elusive.To address this topic, we performed laboratory and greenhouse bioassays with herbivorous mite pests and predatory mites on mutant tomato plants that lack defensive hairs on stems and leaves. Particularly, we investigated the behaviour and population dynamics of different phytophagous mite species in the absence and presence of predatory mites.We show that predatory mites do not only perform better on tomatoes lacking defensive hairs but also that they can suppress herbivore densities better and faster on these hairless plants. Hence, top-down control of herbivores by natural enemies more than compensated the reduced bottom-up herbivore control by plant defences.Our results lead to the counter-intuitive insight that removing, instead of introducing, plant defence traits can result in superior protection against important pests through biological control. Read the free Plain Language Summary for this article on the Journal blog.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia).

Fruit color is one of the most important external qualities of pear (Pyrus pyrifolia) fruits. However, the mechanisms that control russet skin coloration in pear have not been well characterized. Here, we explored the molecular mechanisms that determine the russet skin trait in pear using the F1 population derived from a cross between russet skin ('Niitaka') and non-russet skin ('Dangshansu') cultivars. Pigment measurements indicated that the lignin content in the skin of the russet pear fruits was greater than that in the non-russet pear skin. Genetic analysis revealed that the phenotype of the russet skin pear is associated with an allele of the PpRus gene. Using bulked segregant analysis combined with the genome sequencing (BSA-seq), we identified two simple sequence repeat (SSR) marker loci linked with the russet-colored skin trait in pear. Linkage analysis showed that the PpRus locus maps to the scaffold NW_008988489.1: 53297-211921 on chromosome 8 in the pear genome. In the mapped region, the expression level of LOC103929640 was significantly increased in the russet skin pear and showed a correlation with the increase of lignin content during the ripening period. Genotyping results demonstrated that LOC103929640 encoding the transcription factor MYB36 is the causal gene for the russet skin trait in pear. Particularly, a W-box insertion at the PpMYB36 promoter of russet skin pears is essential for PpMYB36-mediated regulation of lignin accumulation and russet coloration in pear. Overall, these results show that PpMYB36 is involved in the regulation of russet skin trait in pear.

Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation.

BACKGROUND: The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS: In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION: From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.

Study of inhibition of germination of potato by ethylene.

In Canada, the potato (Solanum tuberosum) is by far the most cultivated vegetable and plays a major nutritional role. However, during storage, the potato can easily undergo germination. In this study we have shown the inhibition potential of ethylene as an anti-germinative agent acting especially on phenols. In both varieties assayed (Yukon Gold and Russet Burbank) in this study, the ethylene treatment led to a decrease in total phenol concentration of about 20%. The analysis of potato extracts showed the decrease of specific phenol concentrations which was dependant on the time and temperature of extraction. Our hypothese that the transformation of phenols into phenolic ethyl ethers via possible radical mechanism were then formulated and confirmed by LC and LC/MS.

Russet Susceptibility in Apple is Associated with Skin Cells that Are Larger, More Variable in Size, and of Reduced Fracture Strain.

Russeting is an economically important surface disorder in apple (Malus × domestica Borkh.). Indirect evidence suggests an irregular skin structure may be the cause of the phenomenon. The objective of this study was to characterize epidermal and hypodermal cell morphology and the mechanical properties of the skins of apple cultivars of differing russet susceptibility. Dimensions of epidermal and hypodermal cells were determined using microscopy. Stiffness (S), maximum force (Fmax), and maximum strain (ɛmax) at failure were quantified using uniaxial tensile tests of skin strips. Particularly during early fruit development, epidermal cells (EC) and hypodermal cells (HC) in russet non-susceptible cultivars occurred in greater numbers per unit area than in russet-susceptible ones. The EC and HC were lower in height, shorter in length, and of reduced tangential surface area. There were little differences in S or Fmax between non-susceptible and susceptible cultivars. However, the ɛmaxwere higher for the skins of non-susceptible cultivars, than for those of susceptible ones. This difference was larger for the young than for the later growth stages. It is concluded that russet-susceptible cultivars generally have larger cells and a wider distribution of cell sizes for both EC and HC. These result in decreased ɛmax for the skin during early fruit development when russet susceptibility is high. This increases the chances of skin failures which is known to trigger russeting.

Apple Russet Ring and Apple Green Crinkle Diseases: Fulfillment of Koch's Postulates by Virome Analysis, Amplification of Full-Length cDNA of Viral Genomes, in vitro Transcription of Infectious Viral RNAs, and Reproduction of Symptoms on Fruits of Apple Trees Inoculated With Viral RNAs.

Apple russet ring and apple green crinkle are graft-transmitted diseases first reported more than 60 years ago, but at present, no association between a specific virus (variant) and the disease has been clearly demonstrated. In this study, we conducted the following series of experiments to identify the causal viruses (variants) of these apple diseases; (1) comprehensive analysis by next-generation sequencing of all viruses in each apple tree affected with russet ring or green crinkle disease, (2) amplification of full-length genomic cDNA of viruses using primers containing the T3 promoter and the in vitro transcription of infectious viral RNAs, (3) inoculation of viral RNA transcripts to both herbaceous and apple plants, (4) analysis of sequence variants of viruses present in infected plants, (5) back-inoculation of sequence variants of candidate viruses to apple seedlings combined with the virus-induced flowering technology using the apple latent spherical virus vector to reproduce the symptom on the fruit as soon as possible, and (6) reproduction of symptoms on the fruits of apple trees inoculated with sequence variants and the re-isolation of each virus variant from apples showing fruit symptoms. The results showed that one of the sequence variants of the apple chlorotic leaf spot virus causes a characteristic ring-shaped rust on the fruits of infected apple trees and that a sequence variant of the apple stem pitting virus probably causes green crinkle symptoms on an infected apple fruit. Thus, we were able to fulfill Koch's postulates to prove the viral etiology of both the apple russet ring and green crinkle diseases. We also propose an experimental system that can prove whether a virus found in diseased tissues is the pathogen responsible for the diseases when the etiology is undetermined.

Lignin and Quercetin Synthesis Underlies Berry Russeting in 'Sunshine Muscat' Grape.

In order to further explore the mechanism of 'sunshine muscat' grape russet formation, transcriptomic and metabolomic analyses were performed on 'sunshine muscat' grape peels with and without russet. A total of 1491 differentially expressed genes (DEGs) were discovered based on these analyses. The phenylpropane synthesis pathway was the key metabolic pathway identified, and 28 DEGs related to phenylpropane synthesis pathway were screened, of which 16 were related to lignin synthesis. In addition, 60 differential metabolites were screened. There were 29 phenolic substances among the differential metabolites, which were all up-regulated and 10 were quercetin-related glycosides. Our results indicate that phenols likely play a dominant role in the formation of 'sunshine muscat' grape russet, and the synthesis of lignin and quercetin may be the key factors underlying russet formation.

Genomic analysis of Sweet potato feathery mottle virus from East Africa.

Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.