Lengths, numbers of reads and BlastX analysis results for VANA 454 <i>de novo</i> contigs from sugarcane plants VARX and USDA with detectable homology to mastreviral sequences.

<p>Acronyms used are as follows: SSEV (Sugarcane streak Egypt virus), DDSMV (Digitaria didactyla striate mosaic virus), BCSMV (Bromus catharticus striate mosaic virus), MSV (Maize streak virus).</p

Lengths, numbers of reads and BlastX analysis results for siRNA <i>de novo</i> contigs from sugarcane plant VARX with detectable homology to mastreviral sequences.

<p>Acronyms used are as follows: SSEV (Sugarcane streak Egypt virus), SWSV (Sugarcane white streak virus), SacSV (Saccharum streak virus), WDIV (Wheat dwarf India virus), SSRV (Sugarcane streak Reunion virus).</p

Maximum-likelihood phylogenetic tree of 63 virus isolates representing each known mastrevirus species (including major strains) and the 6 SWSV isolates determined in this study.

<p>Tree branches are coloured according to the geographical origins of the viruses. Branches marked with filled and open circles respectively have >95% and 80–94% approximate likelihood ratio test support; branches having <80% support were collapsed. The phylogenetic tree is rooted using the full genome sequence of Dicot-infecting mastreviruses.</p

Maximum-likelihood phylogenetic tree of Rep (A) and CP (B) proteins.

<p>Tree branches are coloured according to the geographical origins of the viruses. Branches marked with filled and open circles are respectively have >95% and 80–94% approximate likelihood ratio test support; branches having <80% support were collapsed.</p

Size distribution of sequenced siRNAs obtained from the VARX plant.

<p>The histograms represent the numbers of siRNA reads in each size class. (A) The size distributions of total reads, (B) The size distributions of reads mapping to the <i>rep</i> gene C-sense intronic region of SWSV, (C) The size distributions of reads mapping to the V1–V2 ORFs region of SWSV and (D) The size distributions of reads mapping to the C1 ORF region of SWSV.</p

Maximum-likelihood phylogenetic trees depicting the relatedness of cowpea viruses from Burkina Faso.

<p>A) Maximum-likelihood phylogenetic trees of partial <i>cp</i> genes from nine isolates of Cowpea polerovirus 1 and representative species from the family <i>Luteoviridae</i>. SCYLV, Sugarcane yellow leaf virus; PLRV, Potato leafroll virus; PeVYV, Pepper vein yellows virus; CpCSV, Chickpea chlorotic stunt virus; BrYV, Brassica yellows virus; BWYV, Beet western yellows virus; BYDV, Barley yellow dwarf virus; BLRV, Bean leafroll virus; SbDV, Soybean dwarf virus; PEMV-1, Pea enation mosaic virus-1; GRAV, Groundnut rosette assistor virus; PBMYV, Phasey bean mild yellows virus. B) Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> genes from four isolates of Cowpea tombusvirid-1 and representative species from the family <i>Tombusviridae</i>. TurCV, Turnip crinkle virus; MNSV, Melon necrotic spot virus; MCMV, Maize chlorotic mottle virus; JCSMV, Johnsongrass chlorotic stripe mosaic virus; OCSV, Oat chlorotic stunt virus; TNV A, Tobacco necrosis virus A; OLV1, Olive latent virus 1; PMV, Panicum mosaic virus; CMMV, Cocksfoot mild mosaic virus; CarMV, Carnation mottle virus; MWLMV, Maize white line mosaic virus; PNSV, Pelargonium necrotic spot virus; CIRV, Carnation Italian ringspot virus; GaMV, Galinsoga mosaic virus; FNSV, Furcraea necrotic streak virus; LWSV, Leek white stripe virus; BBSV, Beet black scorch virus; SCNMV, Sweet clover necrotic mosaic virus; CRSV, Carnation ringspot virus; CkMV, Cocksfoot mottle virus. C) Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> gene from 5 isolates of CPMoV from Burkina Faso and representative species from Carmovirus genus and from the family <i>Tombusviridae</i>. CCFV, Cardamine chlorotic fleck virus; SYMMV, Soybean yellow mottle mosaic virus; HCRV, Hibiscus chlorotic ringspot virus; PSNV, Pea stem necrosis virus; MNSCG, Melon necrotic spot virus; CymRSV, Cymbidium ringspot tombusvirus; MPV-PM75, Moroccan pepper virus. D: Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> genes from five isolates of SCPMV from Burkina Faso and representative species of the Sobemovirus genus. SCPMV, Southern cowpea mosaic virus; RYMV, Rice yellow Mottle virus; CfMV, Cocksfoot mottle virus_sobemovirus; SCMoV, Subterranean clover mottle virus; SYCMV, Soybean yellow common mosaic virus; SBMV, Southern bean mosaic virus; SeMV, Sesbania mosaic virus; CarMV, Carnation mottle virus. For all four trees, branches associated with a filled dot have bootstrap support above 90 per cent whereas those with an unfilled dot have bootstrap support above 70 per cent. All branches with less than 50 percent bootstrap support were collapsed.</p

Selection of plant virus VANA-contigs and VANA-reads recovered from cowpea plants collected in Burkina Faso.

<p>Selection of plant virus VANA-contigs and VANA-reads recovered from cowpea plants collected in Burkina Faso.</p

List of cowpea-infecting viruses present in Africa.

<p>List of cowpea-infecting viruses present in Africa.</p

Geographical distribution and prevalence of Cowpea viruses in Burkina Faso.

<p>Geographical distribution and prevalence of Cowpea viruses in Burkina Faso.</p

Associations between siRNAs and SWSV/SSEV genomic and transcript secondary structures in the HCSS.

<p>Associations between siRNAs and SWSV/SSEV genomic and transcript secondary structures in the HCSS.</p