Presence of Diverse Sugarcane Bacilliform Viruses Infecting Sugarcane in China Revealed by Pairwise Sequence Comparisons and Phylogenetic Analysis

In silico identification of sugarcane (Saccharum officinarum L.) genome encoded microRNAs targeting sugarcane bacilliform virus

“…A nucleic acid (DNA)-binding protein of the SCBV genome is encoded by ORF2 [ 6 , 45 ]. RNAhybrid and miRanda predicted potential target binding site of ssp-miR166 at locus position 1449–1470 ( Fig 3A and 3C ).…”

“…The poly proteins constitute the largest portion of the SCBV genome encoded by ORF3 [ 2 , 6 ]. Potential candidate miRNAs from sugarcane were identified by the miRanda algorithm to target ORF3, including sof-miR159 (a, b, c, d, and e) at common locus 5534, sof-miR167 (a, b) at locus 2273, sof-miR168b at locus 4588, sof-miR408 (a, b, c, d, and e) at the two common loci of 4595 and 6695, ssp-miR166 at locus 1986, ssp-miR827 at locus 2816, and ssp-miR444 (a, b, and c-3p) at common locus 6184.…”

“…The poly proteins constitute the largest portion of the SCBV genome encoded by ORF3 [2,6]. Potential candidate miRNAs from sugarcane were identified by the miRanda algorithm to…”

“…Infected sugarcane plants have also been monitored and feature no symptoms. In recent years in China, SCBV-infection in sugarcane plants has resulted in a reduced sucrose content, juice, stalk weight, purity, and gravity [ 6 ].…”

“…ORF3 encodes the largest polyprotein, represented as P3 here, and is composed of multiple functional sub-units. The polyprotein (P3) is cleaved by a viral aspartic protease to give rise to multiple functional small proteins, thereby forming intracellular movement, capsids, aspartic proteases, reverse transcriptase (RT), and ribonuclease H (RNase H) [1][2][3][4][5][6]. The RT-RNaseH-coding region is considered to be the most common taxonomic marker for the identification of badnaviral genomic components.…”