Molecular Plant Pathology On-Line [http://www.bspp.org.uk/mppol/1999/0206LOTRAKUL]

Cloning of a DNA-A-like genomic component of sweet potato leaf curl virus : nucleotide sequence and phylogenetic relationships

Lotrakul P and Valverde R A

Department of Plant Pathology and Crop Physiology, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.

Corresponding author: Valverde, R.A. Department of Plant Pathology and Crop Physiology, 302 Life Sciences Bldg., Louisiana State University, Baton Rouge, LA 70803, USA. Telephone : (225)-388-1384 Fax : (225)-388-1415 E-mail:rvalver@lsuvm.sncc.lsu.edu

ABSTRACT

The complete nucleotide sequence of the United States isolate of sweet potato leaf curl geminivirus (SPLCV-US) DNA-A-like genomic component was determined from three overlapping PCR clones. SPLCV-US has genome organization similar to that of monopartite begomoviruses, with six open reading frames (ORFs) and an intergenic region containing a conserved stem-loop motif. The incomplete direct repeat iterons were also found within the intergenic region with positions and arrangement similar to those of begomoviruses from the old world. The presence of the AV2 ORF also supports the relationship of SPLCV-US to old world begomoviruses. The relationships between SPLCV-US and other whitefly-transmitted geminiviruses were investigated by using phylogeny of derived AV1 and AC1 amino acid sequences. Both analyses using neighbor-joining and parsimony gave similar results. The analyses revealed that SPLCV-US has a coat protein which is unique from its counterparts from both the old and new world. Based on the AC1 amino acid sequence, SPLCV-US was found to be more closely related to begomoviruses from the old world, although its position on the phylogenetic branch is still uncertain. The relationship with other old world begomoviruses was further determined by phylogenetic analysis using the AV2 amino acid sequence which revealed that SPLCV-US is closely related to cowpea golden mosaic virus and mungbean yellow mosaic virus.