Rajarshi Kumar Gaur

Molecular characterization and recombination analysis of an Indian isolate of Onion yellow dwarf virus

This study presents the first whole genome sequence of Onion yellow dwarf virus (OYDV isolate RR1) from onion (Allium cepa) in India along with phylogenetic and recombination studies. We examined the sequence variability, distribution of simple sequence repeats (SSRs), and recombination breakpoints of different OYDV geographical isolates. The P1 and P3 regions of OYDV show a higher rate of sequence variability in amino acid and nucleotide sequences than other genomic regions. Entropy peaks of deduced amino acid sequences were higher in both regions (P1 and P3) of different OYDVs. The observed frequency of microsatellites was also higher in the P3 region of all OYDV genomes. The Indian isolate RR1 showed 75–98xa0% similarity with the other OYDV isolates in nucleotide and amino acid sequences and has 43 microsatellites and two compound microsatellites. It was most closely related to garlic isolate MS/SW1 from Australia. Isolate RR1 contained six recombination breakpoints in different genomic regions with the major parent related to the MS/SW1 (Australian) and SG1 (Spanish) OYDV isolates. The phylogenetic and recombination study demonstrated the divergence of Indian isolate RR1 from OYDV isolate from Australia.

Analysis of genome comparison of two Indian isolates of Cowpea aphid-borne mosaic virus from India.

The complete sequence of two Cowpea aphid-borne mosaic virus (CABMV) isolates (RR3 and RR4) from India was determined. Phylogenetic analysis showed that both isolates showed different closeness with other isolates of CABMV. CABMV-RR3 showed maximum identity of 99xa0% with CABMV-BR1 from Brazil at nucleotide and protein levels, whereas CABMV-RR4 showed identity of 73 and 95xa0% with CABMV-Z isolate from Zimbabwe at nucleotide and protein levels respectively. Similarity identity matrix revealed 69xa0% identity at nucleotide level and 91xa0% at protein level with each other. Recombination breakpoint detection showed that CABMV-MG-Avr from Brazil and CABMV-Z from Zimbabwe act as major parents in our isolates RR3 and RR4, respectively.

Systemic Infection of Potyvirus: A Compatible Interaction Between Host and Viral Proteins

Viruses profoundly depend on endogenous host transport system and interact with preexisting host cellular factors during movement. Potyviral movement is directed by several movement proteins that are HC-Pro, CP, VPg, and CI and newly discovered P3N-PIPO. CP and HC-Pro facilitate movement of virus by increasing size exclusion limit (SEL) of plasmodesmata (PD). These movement proteins serve many functions: binding the viral genome, transporting the viral genome to plasmodesmata, gating plasmodesmata, trafficking through plasmodesmata, and then transporting through phloem. TuMV P3N-PIPO is a PD-localized protein and mediates the targeting of CI to PD. The P3 protein was not previously associated with potyvirus movement, but it was known to interact with the P1 protein; it is co-localized with 6K2 vesicles (site of potyviral replication). This points out a link between virus replication complexes and intracellular movement. CP has the ability to increase SEL of PD and interact with host RTM factors and suppress RTM resistance of plants. HC-Pro is crucial for long-distance movement of potyvirus by suppressing gene silencing mechanism of host plant. Interaction with host factors and chaperones is also required for efficient spread of potyvirus; presumably interaction of the viral CP with a plant Dna J-like protein NtCPIP (capsid protein interacting proteins) provides a strong in vivo confirmation for the essential role of plant chaperones in potyvirus movement. In this chapter, we are concerned on potyvirus intracellular, intercellular, and long-distance movement, focusing on the host cellular factors’ interaction with movement proteins involved.

Genetic Engineering of Horticultural Crops: Present and Future

Abstract The world faces an invisible health crisis in the form of hidden hunger and micronutrient deficiency, and the concomitant global demand for food is rising continuously. The burgeoning population needs crops engineered to produce more and tolerate climate change. Genetic engineering has revolutionized the entire crop improvement programs by providing crops with improved nutritional value, biotic and abiotic stress tolerance, therapeutic and industrial proteins, and superior agronomic traits. In the last decade, genome editing with designer nucleases has had a great impact on crop breeding as well as on human lives. In this chapter, we attempt to summarize the transgenic technologies and their potential applications in the improvement of horticultural crops. The future challenges and opportunities for the deployment of genetic engineering and genome editing technologies in horticultural crop improvements are also discussed.

Current Knowledge of Viruses Infecting Papaya and Their Transgenic Management

Papaya (Carica papaya L.), native to the South American continent, is an important horticultural crop cultivated across the tropical and subtropical regions of the globe. Papaya is rich source of vitamin-C and globally it is ranked fourth in total fruit production, next only to bananas, oranges and mangoes. India is the leading producer of papaya and both India and Brazil put together account for more than 50 % of global papaya production. Multiple pests and pathogens are known to inflict damage to papaya, of which viral diseases are the most damaging ones. Of all the viral diseases, papaya ring spot virus (PRSV) belonging to the Potyviridae family is most important one, followed by the viruses belonging to the Geminiviridae family causing leaf curl disease in papaya. Other viral diseases of papaya are Papaya meleira virus (PMeV), Papaya mosaic virus (PapMV), Papaya lethal yellowing virus (PLYV) and several other viruses are known to infect papaya, but may not be of economical significance. Management of viral diseases in papaya is very crucial to accomplish a good harvest, and of all the management practices, genetic engineering papaya for virus resistance is most promising and successful. The PRSV resistant transgenic papaya varieties “SunUp” and “Rainbow” developed by the University of Hawaii and extensively cultivated in the Hawaii islands of United States is the most successful field application of transgenic technology. Since there is significant sequence variation in the PRSV strains from different parts of the world and many more diverse range of viruses are known to infect papaya, there is an urgent need to develop region specific virus resistant papaya.

GENETIC VARIABILITY OF THE REPLICASE (NIB) GENE OF PAPAYA RINGSPOT VIRUS IN NORTHERN INDIA INDICATES COMMON ANCESTRY WITH ISOLATES FROM CHINA AND TAIWAN

The purpose of the present study was to investigate the genetic variability and phylogeny of papaya ringspot virus (PRSV) on the basis of NIb (replicase) gene. The NIb and coat protein (CP) regions of about 2.5 kb of seven PRSV isolates from North India were cloned and sequenced. The North Indian isolates R2R and R5R have higher and lower sequence similarity with other PRSV isolates, respectively. Sequence comparison of NIb gene of 42 PRSV isolates, revealed that the average evolutionary divergence of all sequence pairs were 10.6% and 11.2% at amino acid and nucleotide level, respectively. Transitions were more frequent than transversions in the analyzed sequences. Maximum likelihood phylogenetic tree of combined NIb and CP regions indicated the common ancestry of North Indian isolates with Chinese and Taiwanese isolates. One potential recombination breakpoint in isolate R5R, together with its higher sequence identity and common ancestry with Chinese PRSV isolates, suggest the possible import of the former from the Chinese subcontinent.

Plant Viruses: Evolution and Management

Viruses are very small pathogenic particles made up of nucleoprotein (nucleic acid and protein). The study of plant viruses is so important because they cause diseases to the economically important crops. They cause a great loss to the quality and quantity of the crops. Plant viruses show various types of symptoms such as colour breaking, chlorosis, mottling, vein clearing, vein bending, leaf curl, decrease in size, distorted growth, etc. The plant viruses are very simple and are very host specifi c.

Potato Virus Y Genetic Variability: A Review

Disease caused by potato virus Y (PVY) infection is becoming a major constraint of sustainable potato production throughout the world and causes significant financial loss. Therefore, the improved scientific understanding about PVY population structure, genetic variability, and evolutionary dynamics is required for the development of management strategies against PVY infection. In this chapter we provide updated information about PVY genetic variability and factors that drive PVY evolution. The evolutionary dynamics of PVY seems to be robustly coupled to purifying selection in association with neutral evolution and some sporadic actions of positive selection. Recombination is a major driving force for evolution of PVY genome associated with natural selection and mutation. P1, NIb, CI, and HC-Pro regions of PVY genome showed higher sequence variability, dN/dS ratio, and higher number of mutation sites. Values of genetic distances in analyzed sequences revealed that the variations are distributed throughout of PVY genome. We also analyzed transition /transversion bias in 100 PVY complete genome sequences and obtain that the transitions are more favorable than the transversions. Recombination map of several PVY strains provides new insight in the emergence of new variants of PVY.