Reassortment and concerted evolution in banana bunchy top virus genomes.
The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.
Hu
Jer-Ming
JM
Institute of Ecology and Evolutionary Biology, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan. jmhu@ntu.edu.tw
Fu
Hui-Chuan
HC
Lin
Chia-Hua
CH
Su
Hong-Ji
HJ
Yeh
Hsin-Hung
HH
D001208:Asia; D052658:Babuvirus / Q000235:genetics*; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010139:Pacific Islands; D010802:Phylogeny; D016415:Sequence Alignment; D015534:Trans-Activators / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
D036022:Capsid Proteins; D004268:DNA-Binding Proteins; D015534:Trans-Activators; D014764:Viral Proteins; C113490:coat protein, banana bunchy top virus; C045264:replication initiator protein; D004265:DNA Helicases