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Abstract
The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.
Highlights
Geminiviruses infect a wide array of important crop species and are considered the most economically important group of plant viruses in the tropical and subtropical regions of the world (Rojas et al 2018)
Besides geminivirus replication-associated protein (Rep) homologues previously reported in the genomes of Dioscorea alata, Malus domestica, Lactuca sativa, Coffea canephora, Populus trichocarpa, and Nicotiana sp. (Nicotiana tomentosiformis and Nicotiana tabacum) (Filloux et al 2015; Murad et al 2004), we further identified putative geminivirus Rep homologues within the published genomes of Amborella trichopoda (Amborella), Macadamia integrifolia, Helianthus annuus, Vaccinium corymbosum, Vaccinium macrocarpon, Oryza longistaminata, Olea europaea, Solanum melongena, and Camellia sinensis
endogenous geminivirus-like (EGV) Rep homologues were retrieved from forty-two different angiosperm species (Supplementary Table S3), including homologues solely found in thirteen angiosperm genomes, twenty-seven homologues only found in angiosperm transcriptomes, and homologues found in both the genomes and transcriptomes of two angiosperms (Camellia sinensis and Solanum melongena)
Summary
Geminiviruses infect a wide array of important crop species and are considered the most economically important group of plant viruses in the tropical and subtropical regions of the world (Rojas et al 2018). Geminivirus genomes are composed of one or two components that encode four to eight proteins, the most conserved of which is a replicationassociated protein (Rep) that is required for the initiation of rolling circle replication (Jeske 2009; Filloux et al 2015; Varsani et al 2017) Based on their genome structure, pairwise nucleotide sequence identities, insect vectors, and host plant species, nine genera are currently recognized within the family Geminiviridae (Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus, and Turncurtovirus). Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear genomes of host germline cells, enabling their vertical transmission and potential fixation in host populations (Feschotte and Gilbert 2012; Frank and Feschotte 2017) For viruses such as retroviruses which encode an integrase, endogenization is an active process that is an essential part of the virus life cycle (Silva et al 2017; Santini et al 2018). We have computationally explored publicly available plant genome sequences and plant transcriptomes for the presence of homologues of geminiviral rep genes to both determine the pervasiveness and diversity of EGVs, and explore the potential impacts of newly discovered EGVs on the biology and evolution of the plants species in which they occur
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