plosone-phylo
pone.0019050.g002.png
Genomic and phylogenetic analysis of the virus genomes discovered by VEM.
The tree is midpoint rooted for clarity, all nodes with more than 75% bootstrap support are labeled, and new sequences are indicated by arrows. A) Maximum likelihood phylogeny of the entire DNA-A of the novel Chenopodium leaf curl virus - [USA:Florida:Citra: 2009], Chenopodium leaf curl virus - [USA:Florida:Citra: 2007:VEM] , and Sida golden mosaic Linguanea virus- [USA:Florida:Homestead:2009:VEM] with related begomovirus genome sequences. B) Maximum likelihood phylogeny of the entire DNA-B of the Sida golden mosaic virus - [USA:Florida:Citra:2007:VEM] and Whitefly VEM Begomovirus - [USA:Florida:Homestead:2009:VEM]. Begomovirus names are abbreviated according to convention. C & D) Genome characteristics and organization of the DNA-A, DNA-B and satellite DNA identified in the Citra and Homestead samples. The ORFs encode for: CP/AV1, coat protein; Rep/AC1, replication-associated protein; TrAP/AC2, transcription activator and/or silencing suppressor; REn/AC3, replication enhancer; MP/AV2, movement protein; AC4, AC4 protein; AC5, AC5 protein; MP/BC1, movement protein; NSP/BV1, nuclear shuttle protein. The positions of sequence fragments recovered in the virome, the conserved stem loop and nonanucleotide sequence are indicated.
pone.0019050.g002.png
Genomic and phylogenetic analysis of the virus genomes discovered by VEM.
The tree is midpoint rooted for clarity, all nodes with more than 75% bootstrap support are labeled, and new sequences are indicated by arrows. A) Maximum likelihood phylogeny of the entire DNA-A of the novel Chenopodium leaf curl virus - [USA:Florida:Citra: 2009], Chenopodium leaf curl virus - [USA:Florida:Citra: 2007:VEM] , and Sida golden mosaic Linguanea virus- [USA:Florida:Homestead:2009:VEM] with related begomovirus genome sequences. B) Maximum likelihood phylogeny of the entire DNA-B of the Sida golden mosaic virus - [USA:Florida:Citra:2007:VEM] and Whitefly VEM Begomovirus - [USA:Florida:Homestead:2009:VEM]. Begomovirus names are abbreviated according to convention. C & D) Genome characteristics and organization of the DNA-A, DNA-B and satellite DNA identified in the Citra and Homestead samples. The ORFs encode for: CP/AV1, coat protein; Rep/AC1, replication-associated protein; TrAP/AC2, transcription activator and/or silencing suppressor; REn/AC3, replication enhancer; MP/AV2, movement protein; AC4, AC4 protein; AC5, AC5 protein; MP/BC1, movement protein; NSP/BV1, nuclear shuttle protein. The positions of sequence fragments recovered in the virome, the conserved stem loop and nonanucleotide sequence are indicated.