Arch Virol (2006) 151: 933–946
A phylogenetic survey of recombination frequency
in plant RNA viruses
E. R. Chare
and E. C. Holmes
Department of Zoology, University of Oxford, Oxford, U.K.
Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania
State University, Mueller Laboratory, University Park, Pennsylvania, U.S.A.
Received August 3, 2005; accepted October 4, 2005
Published online November 15, 2005
Summary. The severe economic consequences of emerging plant viruses high-
lights the importance of studies of plant virus evolution. One question of particular
relevance is the extent to which the genomes of plant viruses are shaped by
recombination. To this end we conducted a phylogenetic survey of recombination
frequency in a wide range of positive-sense RNA plant viruses, utilizing 975 capsid
gene sequences and 157 complete genome sequences. In total, 12 of the 36 RNA
virus species analyzed showed evidence for recombination, comprising 17% of the
capsid gene sequence alignments and 44% of the genome sequence alignments.
Given the conservative nature of our analysis, we propose that recombination
is a relatively common process in some plant RNA viruses, most notably the
A variety of factors have been implicated in the emergence of new plant viruses,
including an expanded range of host and vectors, changes in climate and en-
vironment, new agricultural practices and the increasingly global movement of
humans populations and plant products . One evolutionary process that might
facilitate emergence by generating novel variants is recombination. Indeed, re-
combination has already been shown to play a direct role in the emergence of
some geminiviruses  and tobraviruses . Recombination is also of im-
portance in the area of transgenic resistance, which has recently been used to
control some viral diseases of plants [19, 37]. In particular, concerns have been
raised over the theoretical possibility of the creation of novel, chimeric viruses
by recombination between an infecting mutant virus and transgenic plants ex-
pressing wild-type genes of the same or a related virus [2, 15, 17, 18, 36, 47].
Although there is as yet no evidence for recombination between infectious