Sequence analysis of shorter than genome length episomal Banana streak OL virus like sequences isolated from banana in India

Abstract

Electron microscopy and sequencing of reverse transcriptase and ribonuclease H (RT/RNase H) region of Badnavirus genome from two banana cultivars: Poovan (triploid: AAB) and Safed velchi (diploid: AB), exhibiting leaf streak symptoms, confirmed the association of Banana streak OL virus (BSOLV). As per ICTV species demarcation threshold of 80 % identity in RT/RNase H region, both the isolates were identified as BSOLV. Rolling circle and end-to-end amplification showed the association of two short episomal BSOLV variants: BSOLV-IN1 and BSOLV-IN2 from Poovan and Safed velchi banana, respectively. The genome sizes of both isolates were 6,950 nucleotides long, but shorter than the typical BSOLV genome of 7,389 bp. Open reading frames (ORFs) 1 and 2 of shorter BSOLV isolates shared almost complete nucleotide identity (>99 %) to that of BSOLV. However, the ORF 3 (5,130 bp) and intergenic region (IGR), 886 bp, showed deletions compared with ORF 3 (5,499 bp) and IGR (956 bp) of BSOLV. In phylogenetic analysis for ORF 3 polyprotein, both the isolates clustered with BSOLV, Banana streak CA virus (BSCAV), and Sugarcane bacilliform GA virus (SCBGAV). Identical ORF 1, ORF 2, and the presence of all the conserved domains in short ORF 3 and promoter elements in IGR indicated that these isolates represent replicationally competent shorter variants of BSOLV. These two shorter-than-BSOLV genome sequences and two other identical banana streak virus sequences in GenBank (BSV-TRY; DQ859899 and BSV-GD; DQ451009) might have evolved due to error-prone reverse transcription and splicing or excision from the integrated sequences by homologous recombination in natural banana hybrids under field conditions.

Molecular characterization of a new badnavirus associated with streak symptoms on enset (Ensete ventricosum, Musaceae)

“…The amplification of badnavirus‐like sequences in many enset samples shows that badnavirus sequences are frequently integrated into the enset genome as is also the case for crops like banana, sugarcane, taro or yam (Baranwal et al., ; Geering et al., ; Harper, Osuji, Heslop‐Harrison, & Hull, ; Yang et al., ). A recent study on the complete enset genome (Harrison et al., ) demonstrated that the enset genome contains sequences of viral origin.…”

“…The occurrence of both full and deleted versions of a badnavirus genome has been described from Kalanchoë plants infected with Kalancho ë top‐spotting virus (Yang, Nicolaisen, Olszewski, & Lockhart, ). Recently, shorter‐than‐full‐length genomes of two replication competent isolates from Banana streak OL virus on banana have been reported from India (Baranwal, Sharma, Khurana, & Verma, ). Hence, it is possible that the deleted version of ELSV represents a DI‐DNA.…”

Analysis of Banana Viruses with Decision Tree

“…Methodical way is different from other studies that most of them used PCR-based diagnostic method [3], [4], while bio-informatics and decision tree is used in this research [5]. Also, there are clear differences in a regard that we deal with precisely different types of banana streak viruses, such as Banana streak IM virus, Banana streak CA virus, Banana streak UM virus, etc.…”

Partial characterization and development of sensitive and reliablediagnostic for the detection of cucumber mosaic virus

“…It is the largest fruit crop in India, accounting 33% of the total fruit production, and has great socioeconomic significance. The crop is reported to be infected by a number of pests and diseases including a number of viruses such as Banana bunch top virus (BBTV) (Banerjee et al, 2014), Banana streak virus (BSV) (Baranwal et al, 2014), Cucumber mosaic virus (CMV) (Khan et al, 2011), Banana bract mosaic virus (BBrMV) (Balasubramanian and Selvarajan, 2014), Banana mild mosaic virus (BanMMV) (Teycheney et al, 2007), and Banana dieback virus (BDBV) (Hughes et al, 1998). Vegetative propagation of the banana crop results in continuation of viruses from one generation to the next generation, decreasing the yield of the products and the health of the plants.…”