Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution

Abstract

A new isolate of Rice tungro bacilliform virus (RTBV) was collected from Chinsura, West Bengal, India. The full genome was sequenced and deposited to GenBank designating the new one as Chinsura isolate. The four open reading frames (ORFs) of the new isolate were compared with those of previously reported 'South-east Asian' (SEA) and 'South Asian' (SA) isolates emphasizing the ORF3, which is the largest and functionally most important gene of RTBV. In the ORFs, Chinsura isolate shared 90.0-100.0% identity at amino acid level with SA isolates, but only 58.76-88.63% identity with SEA isolates for the same. Similarly, the amino acid identity of ORFs between SEA and SA isolates ranged from 58.77 to 88.64, whereas within each group the corresponding value was >96.0%. The phylogenetic analysis based on nucleotide and amino acid sequences of each ORF made two broad clusters of SEA- and SA-types including Chinsura isolate within SA cluster. Moreover, the relative positions and length of functional domains corresponding to movement protein (MP), coat protein (CP), aspartate protease (PR) and reverse transcriptase/ribonuclease H (RT/RNase H) of ORF3 of Chinsura isolate were completely identical with SA isolates. The clustering pattern indicated strong influence of geographical habitat on genomic evolution. Comparison of ORF3 among all the isolates revealed major variations at non-functional regions in between the functional domains and at the hypervariable 3'-terminal end of ORF3, while PR appeared to have evolved differentially in SA isolates expecting further characterization.

Molecular characterisation of rice tungro bacilliform virus isolated from Bario, Sarawak

“…RTBV isolates are grouped according to their geographical distribution based on their nucleotide sequences into South Asia (SA) and Southeast Asia (SEA) clusters (Fan et al, 1996;Banerjee et al, 2011). For the purpose of this study, nucleotide sequences of CP gene of RTBV from 25 isolates representing both clusters were retrieved from NCBI GenBank for the phylogenetic analysis.…”

The large intergenic region of Rice tungro bacilliform virus evolved differentially among geographically distinguished isolates

“…Therefore, the same mechanisms might be involved for the deletions in the LIGR of SA isolates of RTBV. The shorter LIGR of SA isolates was somewhat responsible for the reduction in genome length of SA isolates as all the ORFs possessed more or less identical length in all RTBV isolates [29]. The LIGR, without coding any functional gene or protein, is of major significance as a dweller of promoter and leader sequence of RTBV.…”

“…For the analysis described in this paper, the LIGR of same eleven RTBV isolates which were used in our previous study [29] was taken. The pair-wise multiple alignments of LIGR as well as leader sequence were performed using the CLUSTAL W algorithm in MegAlign TM program of Lasergene software Fig.…”

“…In our previous investigation we have reported a new SA type isolate of RTBV from India (Chinsura isolate) and demonstrated strong influence of geographical distribution on genomic evolution particularly comparing the ORFs between SEA and SA type [29]. It has been found that the SEA and SA isolates shared \89.0% amino acid identity in the coding region, whereas within each group the corresponding value was [96.0%.…”

Variasi Genetik Rice tungro bacilliform virus (RTBV) dari Daerah Istimewa Yogyakarta, Nusa Tenggara Barat, dan Sulawesi Tengah

“…Analisis homologi ORF terhadap beberapa isolat RTBV dari daerah endemis di India menunjukkan adanya keragaman genetik antarisolat (Banerjee et al 2012;Mangrauthia et al 2012). Isolat RTBV di India tergabung dalam satu kelompok dengan isolat-isolat Asia Selatan dan terpisah jauh dari isolat dari beberapa negara Asia Tenggara, seperti Thailand, Malaysia, dan Filipina (Banerjee et al 2011;Sharma et al 2011).…”