Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus

Abstract

Sugarcane bacilliform virus (SCBV), a plant pararetrovirus causing leaf eck disease in sugarcane across the globe. Since the virus occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among the virus isolates from 104 isolates infecting germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, ve novel genotypes are being proposed: SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y. SCBV-W: CBJ 46, due to the divergence in the nucleotide and protein sequence with existing isolates, established itself as a novel candidate in SCBV species. In comparison with the existing database of SCBV and conclusion from the present study, SCBV isolates from India exhibited maximum diversity in comparison with other regions. SCBV-U, SCBV-W, SCBV-X which turned out as potent recombinants along with other six recombinants in the study, directs at the plausible heterogeneity and genetic exchange happened within SCBV species over time which lead to the evolution of new variants. Neutrality tests indicate the existence of low-frequency polymorphism and Selection pressure of < 1 pointed out at purifying selection. Codon usage bias acted as an e cient tool for identifying patterns in SCBV, in which non-randomness in mutational events might lead to the over expression of codon AGA. The current study on characterization and evidence of nucleotidal variation within SCBV species will lead to devising robust diagnostics of the virus in quarantine and improving the knowledge on the evolutionary changes in SCBV species.

Identification of a sugarcane bacilliform virus promoter that is activated by drought stress in plants

“…The other nine isolates were retrieved from GenBank: SCBV-BRU (JN377537), SCBIMV-QLD (NC_003031), SCBV-BT (JN377536), SCBV-BO91 (JN377533), SCBV-Iscam (JN377534), SCBV-BB (JN377535), SCBGDV-Batavia (FJ439817), SCBGAV-R570 (FJ824813), SCBGAV-B51129 (FJ824814). Classification of SCBV genotypes was performed according to Janiga et al 16 . Each phylogenetic tree was constructed using the neighbor-joining (NJ) method and bootstrap values (1000 replicates) are indicated at tree nodes.…”

“…In petunia, overexpression of gene LeNCED1 (related to the ABA biosynthesis pathway) with inducible promoter rd29A improved drought resistance and lacked negative pleiotropic effects on plant growth and development that was observed with constitutive promoter CaMV 35S 42 . Because endogenous viral elements are widespread in plant genomes and because badnaviruses can be integrated in their host genome, SCBVs that exhibit high genetic diversity are good candidates for identification of alternative promoters and their use in plant genetic engineering 9 , 16 , 43 . The features of stress-expression of SCBV promoters remain unclear.…”

“…Sugarcane bacilliform viruses (SCBV; genus Badnavirus , family Caulimoviridae ) that are associated with leaf fleck in sugarcane possess circular, double-stranded DNA genomes encoding three open reading frames (ORFs) 14 , 15 . These viruses show high genetic diversity and 25 different genotypes (SCBV-A to SCBV-Y) have been reported so far 16 . In the family Caulimoviridae , the intergenic region of the viral genome is a potential promoter region (PPR) 9 , 17 .…”

Emerging and Re-Emerging Diseases Caused by Badnaviruses

“…Similarly, based on the RT/RNaseH region sequence analysis of 63 SCBV-infected sugarcanes from different regions of China, they were grouped into nine SCBV phylogroups of which phylogroups SCBV-S and SCBV-T were newly proposed [ 124 ]. Later, Janiga et al [ 134 ] added five more phylogroups (SCBV-U to SCBV-Y) based on the RT/RNaseH region sequencing of 104 SCBV-infected sugarcane germplasms and Saccharum hybrids from India. Recently the occurrence of SCBV and its variability was reported in Ethiopia [ 135 ].…”

“…The occurrence of recombinant strains within SCBV and between SCBV and BSV strains was reported [ 133 , 136 ]. The putative species SCBV-U, SCBV-W, and SCBV-X and six other species were found to be recombinants, indicating the genetic exchange occurring between SCBV species over time, leading to the evolution of new strains/species [ 134 ]. The intergenic region was considered to be the hotspot for recombination followed by ORF1.…”