Figure 1.
Examples of symptoms of ‘affected’ carrot samples (a) Cross section of carrot root showing internal necrosis around the root core.
(b) Internal necrosis of carrot root along the root core. (c) External necrosis of the root tip. (d) Unaffected carrot.
Figure 2.
Percent virus incidence in carrot roots from the total field sample of 102 affected and 99 unaffected carrots for the presence of viruses including CYLV, presented as a percentage of carrots with necrosis symptoms (affected) and without necrosis symptoms (unaffected) where virus was detected by PCR or TaqMan.
Figure 3.
MEGAN derived Phylogram showing the putative identification of contigs in the Sequencing data.
Circle size is derived from the number of contigs assigned to each taxa Red: affected, Green: unaffected.
Figure 4.
Bootstrapped neighbour joining tree of HSP70 proteins from viruses within the family Closteroviridae constructed with MEGA5 using 500 replicates.
Figure 5.
Bootstrapped neighbour joining tree of RNA2 polyproteins from viruses within the family Secoviridae constructed with MEGA5 using 500 replicates.
Figure 6.
Bootstrapped neighbour joining tree of coat proteins from viruses within the family Betaflexiviridae constructed with MEGA5 using 500 replicates.
Table 1.
Relative abundance (Reads per kilobase of viral genome per million sequenced reads-RPKM) of select viruses in sequenced affected and unaffected samples.
Table 2.
Estimates of prevalence of virus and necrosis and the effect of virus removal on reducing necrosis (values in brackets are 95% confidence intervals).