Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.
The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called 'Florendovirus', members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20-34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia.
Andrew D W
AD
Geering
INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
Florian
F
Maumus
1] Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA [2] International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, The Philippines.
Dario
D
Copetti
INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
Nathalie
N
Choisne
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
Derrick J
DJ
Zwickl
INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
Matthias
M
Zytnicki
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia.
Alistair R
AR
McTaggart
Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli, Via J Linussio 51, 33100 Udine, Italy.
Simone
S
Scalabrin
Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
Silvia
S
Vezzulli
1] Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA [2] International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, The Philippines.
Rod A
RA
Wing
INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
Hadi
H
Quesneville
CIRAD UMR AGAP, Station de Neufchâteau, Sainte-Marie, 97130 Capesterre Belle-Eau, Guadeloupe, France.
Pierre-Yves
PY
Teycheney
D052639:Caulimoviridae / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D012275:Oryza / Q000821:virology*; D010802:Phylogeny; D014779:Virus Replication / Q000235:genetics