title: Phylogeny and synonymous codon usage pattern of Papaya ringspot virus coat protein gene in the sub-Himalayan region of north-east India.
abstract: Sub-Himalayan West Bengal is favorable for the production of several fruits and vegetables. Papaya is one of the common plants cultivated in the area. Most of the papaya plants of the area are susceptible to Papaya ringspot virus (PRSV). Coat protein genes of 6 PRSV isolates of the area were sequenced following RT-PCR. Phylogenetic study of the PRSV isolates showed about 80%-90% similarity with Cuban isolates. The codon usage pattern of our isolates was also analyzed, along with several other isolates. PRSV isolates of our study showed a preference for 8 putative optimal codons. Correspondence analysis of the genes of different isolates along the first 2 major axes were done, as the first 2 axes contributed more in shaping codon usage pattern. In the phylogenetic tree constructed by the neighbour-joining method, our isolates clustered together with the east Indian, north Indian, and Bangladeshi isolates. The diversity and codon usage pattern of the PRSV isolates of different regions were studied, and it was observed that the codon usage pattern of PRSV isolates is probably influenced by translational selection along with mutational bias.
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Prosenjit
authors.initials: P
authors.lastname: Chakraborty
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Shibu
authors.initials: S
authors.lastname: Das
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Bikram
authors.initials: B
authors.lastname: Saha
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Piyali
authors.initials: P
authors.lastname: Sarkar
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Arup
authors.initials: A
authors.lastname: Karmakar
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Arnab
authors.initials: A
authors.lastname: Saha
authors.affiliation: b Department of Biotechnology, University of North Bengal, Siliguri 734013, India.
authors.forename: Dipanwita
authors.initials: D
authors.lastname: Saha
authors.affiliation: a Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Aniruddha
authors.initials: A
authors.lastname: Saha
mesh_terms: D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D029441:Carica / Q000821:virology*; D003062:Codon; D007194:India; D010802:Phylogeny; D017800:Potyvirus / Q000145:classification* / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D003062:Codon; C073700:coat protein, Papaya ringspot virus
keywords: analyse des correspondances; biais mutationnel; codon preference; codon usage; correspondence analysis; mutational bias; préférence de codons; sélection traductionnelle; translational selection; usage de codons