Image_2_Mixed infection of an emaravirus, a crinivirus, and a begomovirus in Pueraria lobata (Willd) Ohwi.TIF

Pueraria lobata (Willd) (Pueraria montana var. lobata (Willd.) Maesen & S. M. Almeida ex Sanjappa & Predeep) is an important herbal medicine used in many countries. In P. lobata plants showing symptoms of mosaic, yellow spots, and mottling, mixed infection of new viruses provisionally named Pueraria lobata-associated emaravirus (PloAEV, genus Emaravirus), Pueraria lobata-associated crinivirus (PloACV, genus Crinivirus), and isolate CQ of the previously reported kudzu mosaic virus (KuMV-CQ, genus Begomovirus) was confirmed through high-throughput sequencing. PloAEV has five RNA segments, encoding a putative RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, movement protein, and P5, respectively. PloACV has two RNA segments, encoding 11 putative proteins. Only PloAEV could be mechanically transmitted from mixed infected symptomatic kudzu to Nicotiana benthamiana plants. All three viruses were detected in 35 symptomatic samples collected from five different growing areas, whereas no viruses were detected in 21 non-symptomatic plants, suggesting a high association between these three viruses. Thus, this study provides new knowledge on the diversity and molecular characteristics of viruses in P. lobata plants affected by the viral disease.</p

Table_1_Mixed infection of an emaravirus, a crinivirus, and a begomovirus in Pueraria lobata (Willd) Ohwi.docx

Pueraria lobata (Willd) (Pueraria montana var. lobata (Willd.) Maesen & S. M. Almeida ex Sanjappa & Predeep) is an important herbal medicine used in many countries. In P. lobata plants showing symptoms of mosaic, yellow spots, and mottling, mixed infection of new viruses provisionally named Pueraria lobata-associated emaravirus (PloAEV, genus Emaravirus), Pueraria lobata-associated crinivirus (PloACV, genus Crinivirus), and isolate CQ of the previously reported kudzu mosaic virus (KuMV-CQ, genus Begomovirus) was confirmed through high-throughput sequencing. PloAEV has five RNA segments, encoding a putative RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, movement protein, and P5, respectively. PloACV has two RNA segments, encoding 11 putative proteins. Only PloAEV could be mechanically transmitted from mixed infected symptomatic kudzu to Nicotiana benthamiana plants. All three viruses were detected in 35 symptomatic samples collected from five different growing areas, whereas no viruses were detected in 21 non-symptomatic plants, suggesting a high association between these three viruses. Thus, this study provides new knowledge on the diversity and molecular characteristics of viruses in P. lobata plants affected by the viral disease.</p

Primary and secondary structures of <i>citrus bark cracking viroid</i> (CBCVd) sequences from sub-clades A, B, C, D, E, and F and CBCVd reference sequence (NC003539).

<p>The mutations of CBCVd sequences from these sub-clades were shown in box.</p

Nucleotide diversity of <i>citrus bark cracking viroid</i> (CBCVd) sequences from Pakistan, China, and other countries^a.

<p>Nucleotide diversity of <i>citrus bark cracking viroid</i> (CBCVd) sequences from Pakistan, China, and other countries^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198022#t003fn001" target="_blank">a</a>}.</p

Transcriptome sequencing reveals novel <i>Citrus bark cracking viroid</i> (CBCVd) variants from citrus and their molecular characterization - Fig 1

<p><b>Transcriptome reads mapped onto sequences of CBCVd-P3-1 (A) and P5-1 (B) in PCV-I and PCV-II libraries.</b> Dots represent mismatches of reads.</p

Transcriptome sequencing reveals novel <i>Citrus bark cracking viroid</i> (CBCVd) variants from citrus and their molecular characterization

<div><p><i>Citrus bark cracking viroid</i> (CBCVd), previously called <i>Citrus viroid IV</i>, belongs to the genus <i>Cocadviroid</i> within the family <i>Pospiviroidae</i>. CBCVd has been identified as an important causative agent in citrus and hops. In this study, we obtained the full-length genomes of different variants of all detected citrus viroids from Pakistan through transcriptome sequencing. Different CBCVd variants were first found in Pakistan. These newly discovered Pakistani CBCVd variants were provisionally called “CBCVd-LSS” for their low sequence similarity (80.9%–88.9%) with the CBCVd RefSeq sequence (NC_003539). The two most predominant CBCVd sequences from Pakistan had the closest identity, 90.6% and 87.9%, with two CBCVd sequences isolated from hops. Identification and molecular characterization of CBCVd from citrus in Pakistan and China were also reported. The length of CBCVd from China ranged from 282 to 286 nucleotides, while that of the one from Pakistan ranged from 273 to 277 nucleotides. Based on genetic diversity and phylogenetic analysis, two main CBCVd clades were identified. CBCVd sequences from Pakistan, China, and other countries were further divided into six sub-clades. Sequence alignment revealed some nucleotide changes between these sub-clades, and analysis indicated that several mutations could significantly affect the primary and secondary structure of the viroid. Our results indicated that the CBCVd sequences from Pakistan and China were significantly different with respect to genome and secondary structure and Pakistan might be one of the independent geographical origins of CBCVd worldwide.</p></div

Genomic diversity of <i>citrus bark cracking viroid</i> (CBCVd) isolates from Pakistan and China.

<p>Genomic diversity of <i>citrus bark cracking viroid</i> (CBCVd) isolates from Pakistan and China.</p

Phylogenetic analysis of <i>citrus bark cracking viroid</i> (CBCVd) sequences.

<p>The phylogenetic tree was constructed with genomic sequences of 8 Pakistani CBCVd sequences (indicated by solid triangle), 14 Chinese CBCVd sequences (indicated by solid rectangle), and 26 CBCVd sequences including two variant sequences on hop (indicated by hollow triangle) and the CBCVd RefSeq sequence (indicated by hollow rectangle) available in GenBank. Values below 70% were cut off.</p

Blast results of contigs for samples (PCV-I, PCV-II, respectively) against viroid sequences available in NCBI.

<p>Blast results of contigs for samples (PCV-I, PCV-II, respectively) against viroid sequences available in NCBI.</p

Presentation1.PDF

<p>A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180–210 nm length and 35–40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers P. alienus. The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3′ leader RNA and a 258-nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus Nucleorhabdovirus. Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper P. alienus transmission.</p