Bamboo-Leaf Prickly Ash extract: A potential bio-pesticide against oriental leaf worm, Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae).

Bamboo-Leaf Prickly Ash, Zanthoxylum armatum (Rutaceae) is a versatile and widely distributed plant species in nature. It is an edible plant species, commonly used in daily life for condiments and therapeutic remedies. Besides its bioactive and medicinal properties, different plant parts of the Z. armatum also have insecticidal potential. However, this potential has not been yet determined against many agricultural pests, including leaf worm, Spodoptera litura (Lepidoptera: Noctuidae). In this study, we demonstrated for the first time the contact and oral toxicity and sub-lethal effects (including antifeedent and ovicidal action) of various fractions of pericarp, leaf and seeds of Z. armatum against S. litura. Overall findings revealed that the n-hexane pericarp extract of Z. armatum has strong antifeedent, ovicidal and larvicidal properties against S. litura. Sub-lethal doses of pericarp extract can negatively alter the biology of S. litura. Since n-hexane extract of leaves also has better larvicidal properties, it could also be utilized for the S. litura management during period of unavailability of fruits (or pericarp). Accordingly, the Z. armatum pericarp and leaf extract has tremendous commercial utilization potential for the management of polyphagus pests like S. litura and other related species, which are quite difficult to manage even by chemical pesticides.

Genetic characterization of chayote [Sechium edule (Jacq.) Swartz.] landraces of North Eastern Hills of India and conservation measure.

Chayote or chow-chow is an underutilized cucurbit vegetable crop, widely cultivated by farmers in the backyards and Jhum lands for its tender leaves, fruits and tuberous root. In order to initiate crop improvement program in this crop, the present study was undertaken to assess the genetic variations in the 74 chow-chow landraces collected from the North Eastern Hill region of India. Wide variations for fruit colors, fruit length (6.5-21.5 cm), fruit width (4.2-10.7 cm), fruit weight (60-560 g), vitamin-C (2.6-13.8 mg/100 g), reducing sugar (0.18-2.77%), total sugar (1.09-2.94%) and phenol content (0.17-3.85 mg/100 g FW) were recorded among the landraces. All the landraces were also characterized using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers. In RAPD analyses, out of 28 primers a total of 198 reproducible amplicons were formed at an average of 7.01 per primer and an overall polymorphism of 88.38%. Eight fragments were specific to landraces with light green fruits. Four fragments were observed to be specific to RCSC-22 (dark green fruits) and another four specific to a RCSC-30 (pale yellow fruits). Out of 30 ISSR, only 5 primers generated a total of 32 reproducible amplicons with an average of 6.4 per primer and overall polymorphism of 62.5%. The pair wise similarity coefficient values ranged from 0.55 to 0.96. The grouping of landraces in cluster analysis was found to be independent of their respective geographic locations. The cuttings of suckers and shoot top (2 months old) treated with indole-3-butyric acid (200 mg l-1) provide an alternative for the conservation of the diverse genetic materials to the researchers.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus.

Chilli veinal mottle virus (ChiVMV) causes significant economic loss to chilli cultivation in northeastern India, as well as in eastern Asia. In this study, we have developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid, sensitive and specific diagnosis of ChiVMV. Amplification could be visualized after adding SYBR Green I (1000×) dye within 60 min under isothermal conditions at 63 °C, with a set of four primers designed based on the large nuclear inclusion protein (NIb) domain of ChiVMV (isolate KC-ML1). The RT-LAMP method was 100 times more sensitive than one-step reverse transcription polymerase chain reaction (RT-PCR), with a detection limit of 0.0001 ng of total RNA per reaction.

Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.

Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.

First Record of Rhizoctonia solani AG 1-IB on Mucuna pruriens in India.

Mucuna is the source of L-Dopa (L 3,4 dihydroxyphenylalanine), a precursor of a dopamine used to treat Parkinson's disease. Leaf blight symptoms were observed on Mucuna pruriens plants in October to November 2010 in a field at the Indian Council of Agricultural Research Complex for the Northeastern Hill Region, Umiam, Meghalaya, India. Symptoms included black necrotic areas on leaves, collapsed leaf tissue and, occasionally, fungal growth visible on the leaf. In advanced infections, dead leaves were attached to the stem, followed by defoliation with only infected pods still attached. Approximately 10% of plants were infected in ~0.5 ha surveyed. Symptomatic leaf pieces were washed with sterile water, surface-sterilized using 4% NaOCl for 30 s, washed again, blotted dry, and plated on PDA amended with streptomycin (100 ppm). Characteristics of three fungal isolates were typical of Rhizoctonia solani J.G. Kühn [teleomorph = Thanatephorus cucumeris (A. B. Frank) Donk], i.e., hyphal branching at 90° angles, basal constriction at the hyphal branching point with a septum close to the lateral hyphum (3), and presence of multinucleate hyphal cells confirmed using DAPI (2-(4-amidinophenyl)-1H-indole-6-carboxamidine) staining (1). A culture was deposited at the Agharkar Research Institute, Pune, India (NFCCI No. 2602). The ITS1-5.8S-ITS2 region of nuclear rDNA of one isolate was sequenced after amplification with primers ITS1 and ITS4 (4), (GenBank Accession No. JQ675536). A BLAST search revealed 99% similarity of the sequence with that of 2 R. solani AG 1-IB isolates (AB122137 and AB000039). Sequences were aligned using MAFT Version 6. Maximum parsimony analysis using MEGA 5 placed the test isolate in AG 1-IB with 99% bootstrap support. PCR assays with primers for R. solani AG 1-IB produced a DNA band of ~300 bp (2). Koch's postulates were completed by inoculating 5-mm colonized plugs of PDA at the soil line of each of 5 potted, 40-day-old plants of M. pruriens, and covering the base of each plant with moistened cheesecloth. In addition, 3 plants were inoculated with colonized plugs at the junction of the lamina and petiole of 9 leaves/plant, spraying the plants with sterilized water, and covering the plants with polythene for 3 days. In addition, 10 detached leaves were inoculated with colonized PDA plugs and incubated in a moist chamber. Three non-inoculated plants served as a control treatment for the first 2 methods, and 10 leaves as a control treatment for the third method with sterilized PDA plugs. Symptoms of leaf blight (necrosis from base to leaf tip, with abundant fungal growth) developed in 6 to 7 days on plants inoculated at the soil line, 4 days on leaves inoculated at the junction of the lamina and petiole, and 2 to 3 days on detached leaves. Control plants and leaves remained asymptomatic for all 3 methods. R. solani was reisolated from inoculated plants as described above, and confirmed to be AG 1-IB. The fungus was not reisolated from control plants or leaves. To our knowledge, this is the first record of R. solani AG 1-IB causing leaf blight on M. pruriens in India. References: (1) M. M. Kulik and P. D. Dery. Biotech. Histochem. 70:95, 1995. (2) M. Matsumoto. Mycoscience 43:185, 2002. (3) B. Sneh et al. Identification of Rhizoctonia Species. The American Phytopathological Society Press, St Paul, MN, 1991. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, CA, 1990.

Characterization of smallholder pig production system: productive and reproductive performances of local and crossbred pigs in Sikkim Himalayan region.

The present study was conducted to know the smallholder pig production system in tribal areas of Sikkim State, India. Two hundred tribal farmers were selected randomly from the North and East District of the state. Information on socio-economic characteristics of farmers (gender, occupation, educational status, and farming experience), management practices, disease prevalence, and economics in pig production was collected. The study recorded the mean land holding as 1.2 ± 0.8 ha, and the number of pigs per farm was 5.0 ± 0.28. Pigs were mainly kept as a source of income, and 70 % of farmers reared crossbreed pigs. Ninety percent (90 %) of respondents practiced the intensive system of management whereby kitchen wastes along with cooked mixture comprising maize bhusa, mustard oil cake, pseudostem of banana, tuber, stem, and plant leaves were used to feed their animals. About 40.5 % of farmers procured their breeding stock from government farms that had good records and utilized veterinary services like timely vaccination and deworming. The diseases prevalent in the study area were swine fever, diarrhea, helminthoses, sarcoptic mange, pneumonia, etc. The litter sizes at birth (local, 4.3 ± 0.45; crossbreed, 7.2 ± 0.33), at weaning (local, 2.79 ± 0.24; crossbreed, 6.1 ± 0.21), and age at first farrowing (local, 365.39 ± 7.96 days; crossbreed, 337.24 ± 8.79 days) were recorded. Production costs of meat extracted from local and crossbred pigs were 1.08 $/kg and 0.86 $/kg, respectively.

First Report of Leaf Blight of Basella alba Caused by Rhizoctonia solani AG 1-IB in India.

Thick succulent leaves of Malabar spinach (Basella alba L.) are used for human consumption in India. Symptoms of leaf blight were observed on this plant in October 2010 at Umiam, Meghalaya, India. Symptoms started from the lower leaves and spread to the upper part. Water-soaked lesions covered the whole leaf and gradually the leaves shredded and got detached from the plants. Whole plants were seen defoliated due to severe infection. Lesions were visible on the stem also. The pathogen was isolated on potato dextrose agar amended with streptomycin (100 ppm). Fungus isolated from infected plants had typical characters associated with Rhizoctonia solani J. G. Kühn [teleomorph Thanatephorus cucumeris (A.B. Frank) Donk], i.e., hyphal ramification angles of ~90°, basal constriction, and a septum next to the lateral hyphae (2). Nuclear staining with DAPI (2-(4-amidinophenyl)-1H-indole-6-carboxamidine) confirmed that hyphal cells were multinucleate (1). Molecular analysis was conducted using sequence data (JQ675535) containing ITS1 and 5.8S and ITS 2 of nrDNA, which was obtained after amplification using universal primers ITS1 and 4. BLAST search revealed 99 to 100% similarity with AG 1-IB (GU585667, GU270581). Living culture has been deposited in Agharkar Research Institute, Pune, India (NFCCI No. 2601). Phylogenetic analysis was also conducted using MEGA 5. It also placed the isolate in AG 1-IB clade with 99% bootstrap support in MP (maximum parsimony) analysis. Three healthy plants were inoculated using colonized PDA bits from actively growing culture. Sterilized PDA bits were kept on control plants. Plants were sprayed with water and covered with cheesecloth for 3 days. Inoculated plants developed symptoms after 5 days whereas control plants remained healthy. Inoculations were also done on detached leaves kept in a moisture chamber using colonized PDA bits. In this case, symptoms developed within 3 days. Detached leaves with sterilized PDA bits remained healthy. R. solani was also reisolated from inoculated plants. To our knowledge, this is the first record of AG 1-IB based on molecular evidence on B. alba from India. This new host may accelerate the spread of this pathogen to other crops. References: (1) M. M. Kulik and P. D. Dery. Biotech. Histochem. 70:95, 1995. (2) B. Sneh et al. Identification of Rhizoctonia species. APS Press, St Paul, MN, 1991.

Studies on the identification and control of pathogen Saprolegnia in selected Indian major carp fingerlings at mid hill altitude.

The Indian major carp cultured in ponds in the North Eastern hilly states of India frequently suffer from fungal disease during winter months resulting in mass mortality. This study examined the pathogenic fungi isolated from farmed raised Indian major carp fingerlings and identified as Saprolegnia. For treatment, the diseased fish were exposed to 4g salt per litre of water for 2 min followed by dip treatment with 5ppm KMnO4 for 10 min, thrice every week for a period of 6 weeks. The treatment resulted in recovery from the disease after 6 weeks from the beginning of treatment. Soon after recovery, the pond management practices such as removal of pond bottom soil, application of lime and replenishment with freshwater were followed in the infected ponds. Our study concluded that rapid decrease in pond water temperature from 22 to 8 degrees C that remains low for months together coupled with increased water pH (9) and decreas dissolved oxygen (4ppm) causes saprolegniasis to the fingerlings of Indian major carps.

First Record of Rhizoctonia solani AG 2-1 on Ctenanthe oppenheimiana in India.

Ctenanthe oppenheimiana (= Maranta oppenheimiana) is a common foliage plant also known as "never never" plant. Plants grow best in high-humidity conditions. Potted plants in Barapani, Meghalaya, India were found to be infected with a foliar disease. Initial symptoms were leaf margin necrosis that expanded to cover large areas of the leaf blade during March and April of 2007. Leaf portions from the margin of infected and healthy tissue were washed with sterile water and then surface sterilized with 4% sodium hypochlorite for 30 s. These bits were again washed twice with sterile water, blotted dry, plated on water agar, and maintained at 25°C. After 24 h, mycelial growth was transferred to potato dextrose agar. Fungal colonies were brown with fluffy, aerial mycelium Hypha was branched at 90° with lateral branches having constriction at the point of origin. Hyphal cells were determined to be multinucleate when stained with 4',6-diamidino-2-phenylindole. Sclerotia were 3 to 5.6 mm in diameter (average 4.1 mm) and were not differentiated into cortex and medulla. The above characteristics were consistent with a Rhizoctonia sp. (2). Anastomosis group (AG) was determined by pairing isolates with tester isolates of R. solani and its subgroups (AG 1-1A, AG 2-1, AG 2-2 IIIB, AG 3, AG 4HG-II, AG 5, AG 6, AG 7, AG 8, AG 9, AG 10, AG 11, AG 12, AG 13, and AG BI) and staining hyphae with Safranin-O 0.03% and KOH 3% solutions. Anastomosis was positive only between the Ctenanthe isolate and AG 2-1 tester strain. (1). The Ctenanthe isolate was grown on potato dextrose broth for 8 days. The broth culture was blended in a Waring blender for 2 min and 10 ml was mixed with 90 ml of sterile water. The mycelium suspension was sprayed on five healthy plants of C. oppenheimiana Noninoculated plants served as a control. Inoculated leaves developed initial symptoms of marginal leaf necrosis after 6 to 8 days and expanded leaf necrosis, similar to the original symptoms, after 12 to 15 days. No symptoms developed on noninoculated plants. R. solani was isolated from leaf lesions of the inoculated plants, confirming Koch's postulate To our knowledge, this is a new report from India. References: (1) G. C. MacNish et al. Phytopathology 83:922, 1993. (2) B. Sneh et al. Identification of Rhizoctonia species. The American Phytopathological Society, St Paul, MN, 1991.

First Report of Leaf Blight of Chinese Ground Orchid (Phaius tankervilliae) Caused by Botrytis cinerea in India.

Chinese ground orchid (Phaius tankervilliae Banks:Blume) is a beautiful, terrestrial orchid, which belongs to the family Orchidaceae. It is used as a cut flower, which lasts for 4 to 5 weeks. This species is considered endangered and rare in nature. In June of 2007, potted plants of P. tankervilliae in Shillong, Meghalaya (northeast India; maximum temperature 24°C, minimum temperature 18°C, and 83.5% relative humidity) exhibited leaf blight. Symptoms included water-soaked lesions and dense, gray mold growing on infected tissues. Thirty-six percent of the plants surveyed were found to have this disease. For isolation, diseased tissue was surface disinfested by soaking it in 0.5% sodium hypochlorite for 1 min, air dried, plated on potato dextrose agar, and incubated at 20°C. Mycelia were initially white but later turned gray. Mature, unicellular, ellipsoid, hyaline conidia (6.3 to 8.2 × 9.6 to 11.4 µm) were formed in botryose heads. Hard, black, irregular-shaped sclerotia (average size 1.8 × 2.3 mm) were formed after 15 days. On the basis of these morphological characters, the pathogen was identified as Botrytis cinerea Pers.:Fr. (1). Pathogenicity was confirmed by spraying plants with a spore suspension (106 spores per ml), which were then maintained under high humidity for 48 h at 20 to 22°C by covering with cheesecloth. Five potted plants were inoculated and five were sprayed with sterile water. Lesions and spore masses that were identical to those observed appeared 5 to 6 days after inoculation. Water-treated control plants remained asymptomatic. B. cinerea was reisolated from inoculated plants. A literature search revealed no previous record of this disease in India. So, to our knowledge, this is the first record of B. cinerea on P. tankervilliae in India. References: (1) M. B. Ellis. Dematiaceous Hyphomycetes. CMI, Kew, Surrey, England, 1971.

Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.

The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.

Evidence of BVDV in Pigs from North Eastern Part of India- Genetic Profiling and Characterisation.

INTRODUCTION: The work has been attempted to detect and genetically characterise the nature of Bovine Viral Diarrhea Virus (BVDV) isolates from the porcine population of the north east. METHODS AND MATERIAL: The samples have been collected over a two year period and are from areas where there is a mixed and integrated rearing of livestock in close proximity. The isolates were identified, cloned and sequenced using BVD specific genomic primers for two important domains viz., E-2 and 5' UTR. RESULTS: Porcine BVD Sequences were analysed phylogenetically. Divergence in 3 sequences is noted in the 5' UTR region that are forming a clear outlier group while E-2 sequences are coming close to BVDV group but forming a separate cluster.

Complete mitochondrial genome sequence of a phytophagous ladybird beetle, Henosepilachna pusillanima (Mulsant) (Coleoptera: Coccinellidae).

Ladybird beetles are generally considered as agriculturally beneficial insects, but the ladybird beetles in the coleopteran subfamily Epilachninae are phytophagous and major plant feeding pest species which causes severe economic losses to cucurbitaceous and solanaceous crops. Henosepilachna pusillanima (Mulsant) is one of the important pest species of ladybird beetle. In this report, we sequenced and characterized the complete mitochondrial genome of H. pusillanima. For sequencing of the complete mitochondrial genome, we used the Ion Torrent sequencing platform. The complete circular mitochondrial genome of the H. pusillanima was determined to be 16,216 bp long. There were totally 13 protein coding genes, 22 transfer RNA, 2 ribosomal RNA and a control (A + T-rich) region estimated to be 1690 bp. The gene arrangement and orientations of assembled mitogenome were identical to the reported predatory ladybird beetle Coccinella septempunctata L. This is the first completely sequenced coleopteran mitochondrial genome from the beetle subfamily Epilachninae from India. Data generated in this study will benefit future comparative genomics studies for understanding the evolutionary relationships between predatory and phytophagous coccinellid beetles.

First report of Turnip mosaic virus occurrence in cole crops (Brssica spp) from Arunachal Pradesh, India.

The occurrence of Turnip mosaic virus (TuMV) in cole crops (Brassica spp) grown in Basar, Arunachal Pradesh, India was confirmed by symptomatology, transmission electron microscopy, reverse transcription-polymerase chain reaction and partial characterization of cytoplasmic inclusion protein and coat protein (CP) domains. Phylogenetic analysis of the partial CP sequences of the new TuMV isolates from Indian mustard (AR-IndM), broad leaved mustard (AR-BrLM) and broccoli (AR-Broc) revealed their closest relationship with members of the World-B genogroup of TuMV. This is the first molecular evidence of TuMV infection in Brassica spp from India.

Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India.

The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, aromatic rice accessions from Nagaland; and P3, chakhao rice germplasm from Manipur [corrected]. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice germplasm of NE India for rice improvement.

Complete genome sequence of classical Swine Fever virus subgenogroup 2.1 from assam, India.

We report the complete genome sequence of a classical swine fever virus (genogroup 2.1), isolated from an outbreak in Assam, India. This particular isolate showed a high degree of genetic variation within the subgenogroup 2.1 and may serve as a potential reference strain of the 2.1 genogroup of classical swine fever virus (CSFV) in the Indian subcontinent.

Complete genome sequence of emerging porcine circovirus types 2a and 2b from India.

We report here the first characterized complete genome sequence of porcine circovirus types 2a and 2b from northeastern states of India. These isolates may serve as a potential reference for the Indian strains of porcine circovirus types 2a and 2b.

First report of Chilli veinal mottle virus in Naga chilli (Capsicum chinense) in Meghalaya, India.

The present study confirms the occurrence of Chilli veinal mottle virus (ChiVMV) under the genus Potyvirus in Naga chilli (Capsicum chinense) in Meghalaya based on mechanical transmission assay, transmission electron microscopy, RT-PCR and sequence analysis. This is the first record of Chivmv in Naga chilli in North-East India.

Identification and characterization of a distinct banana bunchy top virus isolate of Pacific-Indian Oceans group from North-East India.

Banana bunch top virus (BBTV) is considered to be a serious threat to banana production. A new isolate of the virus (BBTV-Umiam) was identified and characterized from local banana mats growing in mid-hills of Meghalaya in North-East India. The complete nucleotide sequence analysis revealed the presence of six full-length ssDNA components (DNA R, DNA U3, DNA S, DNA M, DNA C and DNA N) sharing major common region (CR-M) and a stem-loop common region (CR-SL). BBTV-Umiam showed a unique deletion of 20 nucleotides in the intergenic region of DNA R, the absence of predicted open reading frame (ORF) in DNA U3 and probability for a small ORF in DNA U3 expecting functional evidence at transcriptional level. Phylogenetic analysis based on 88 complete nucleotide sequence of BBTV DNA R available in GenBank generated two broad clusters of Pacific-Indian Oceans (PIO) and South-East Asian (SEA) groups including BBTV-Umiam within PIO cluster. However, BBTV-Umiam was identified as the most distinct member of the PIO group with 100% bootstrap support. This was further supported by the phylogenetic grouping of each genomic component of BBTV-Umiam at the distant end of PIO group during clustering of 21 complete BBTV sequences. BBTV-Umiam shared relatively less nucleotide identity with PIO group for each genomic component (85.0-95.4%) and corresponding ORF (93.8-97.5%) than that of earlier PIO isolates (91.5-99.6% and 96.0-99.3%, respectively). Recombination analysis revealed two intra-component and five inter-component recombination events in BBTV-Umiam, but none of them was unique. Moreover, the isolate was identified as major parental sequence for intra-component recombination event spanning the replication-associated protein encoding region in Tongan BBTV DNA R. The current study indicated differential evolution of BBTV in North-East India (Meghalaya). The natural occurrence of hybrids of Musa balbisiana and M. acuminata in this geographically isolated region could be the contributing factor in accumulating genetic distinctiveness in BBTV-Umiam which need further characterization.