DIVERSIFICATION INTO THE GENUS Badnavirus: PHYLOGENY AND POPULATION GENETIC VARIABILITY

Caio Henrique Loureiro De Hollanda Ferreira,Gaus Silvestre De Andrade Lima,Roberto Ramos-Sobrinho,Iraildes Pereira Assunção,Sarah Jacqueline Cavalcanti Da Silva,Lucas Jobim Jordão,Mayra Machado De Medeiros Ferro

doi:10.28998/rca.v17i2.6286

Caio Henrique Loureiro De Hollanda Ferreira, Gaus Silvestre De Andrade Lima + Show 5 more

Open Access

https://doi.org/10.28998/rca.v17i2.6286

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Abstract

Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly sugarcane- and banana-infecting species. Non-tree-like evolution analysis evidenced putative recombination events among badnaviruses, and at least 23 independent events were detected. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in isolates of 11 badnavirus species. These results showed that mutation and recombination are important mechanisms that acting on badnavirus diversification.

Highlights

IntroductionViruses belonging to the family Caulimoviridae have semicircular, double-stranded (ds)DNA genomes, 7.2-9.2 kbp in length, encapsidated into isometric or bacilliform particles, and which replicate through an RNA intermediate (plant pararetroviruses; Geering and Hull, 2012)
Viruses belonging to the family Caulimoviridae have semicircular, double-strandedDNA genomes, 7.2-9.2 kbp in length, encapsidated into isometric or bacilliform particles, and which replicate through an RNA intermediate
Cacao swollen shoot virus (CSSV) was the badnavirus represented by the higher number of sequences/isolates (12), while 25 species were represented by one only sequence (Table 1)

Summary

Introduction

Viruses belonging to the family Caulimoviridae have semicircular, double-stranded (ds)DNA genomes, 7.2-9.2 kbp in length, encapsidated into isometric or bacilliform particles, and which replicate through an RNA intermediate (plant pararetroviruses; Geering and Hull, 2012). This family is divided into eight genera (Badnavirus, Caulimovirus, Cavemovirus, Petuvirus, Rosadnavirus, Solendovirus, Soymovirus and Tungrovirus) according to host range, insect vector, genomic organization and phylogeny (Geering and Hull, 2012; Bath et al, 2016). The criterion of ≥80% nucleotide sequence identity for the RT/RNaseH domains was established for species demarcation in the genus Badnavirus (Geering and Hull, 2012), and specific primer pairs are largely used to amplify this viral genomic region (Yang et al, 2003). The existence of endogenous badnavirus sequences represents a great challenge for taxonomy and diagnosis of members into this genus

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