Two Cotton Begomoviruses Found in Brazil

The begomoviruses are circular DNA viruses, encapsidated in icosahedral geminate particles, transmitted by whiteflies. A survey on cotton begomoviruses was conducted in two regions of Brazil, in the central region and in the North-East region. Plants showing mosaic and interveinal chlorosis symptoms were collected from Central Brazil, Cerrado area. A partial begomovirus genome was amplified from DNA extracts from leaves with symptoms using the begomovirus universal primers from at least 22 samples. The amplified DNA fragments were directly sequenced and compared to other begomovirus sequences by using blastN algorithm. The sequences shared 94 to 97% nucleotide identity with Sida micrantha mosaic virus (SiMMV). The virus amplified from cotton genotypes LA RN 910 and ‘Plains’ showed  95% identity with  SiMMV isolated from common bean GO60 (GenBank: KC706535.1 and HM357459.3).This virus had been previously found affecting Sida micrantha, common beans, soybean and okra in Brazil. Fiber production was reduced on diseased plants. In the North-East region, cotton plants with chlorotic spots, interveinal chlorosis and leaf distortion were collected at Paraiba State, in 2009. First, partial sequences were obtained and confirmed the presence of a begomovirus. Then, the whole genome, including DNA-A and DNA-B, was amplified using bacteriophage phi-29 DNA polymerase in a rolling circle amplification mechanism, followed by digestion with the single cutting enzyme XbaI. Sequences were obtained and the genome assembled. The genome size and their nucleotide sequences exhibited typical characteristics of New World bipartite begomoviruses. The maximum nucleotide identity with known begomoviruses was 77.8% for DNA-A with Tomato common mosaic virus (ToCmMV); and 67.8%  for DNA-B with Tomato yellow vein streak virus. Thus, this virus can be considered as a new species based on the species demarcation criteria of International Committee on Taxonomy of Viruses, and the name Cotton chlorotic spot virus is proposed.