Phylogeography of Rice yellow mottle virus in Africa

Abstract

The sequences of the coat protein gene of a representative sample of 40 isolates of Rice yellow mottle virus (RYMV) from 11 African countries were analysed. The overall level of nucleotide diversity was high ( ,14 %). Great geographical distances between the sites where isolates were collected were consistently associated with high genetic distances. In contrast, a wide range of genetic distances occurred among isolates spread over short geographical distances. There was no evidence of long-range dispersal. RYMV diversity in relation to land area was eight times greater in East Africa than in West/Central Africa. West/Central African isolates with up to 9 % divergence belonged to a monophyletic group, whereas the East African isolates with up to 13 % divergence fell into distantly related groups. In East Africa, each Tanzanian strain had a specific and restricted geographical range, whereas West/Central African strains had large and partially overlapping geographical distributions. Overall, our results suggest an earlier RYMV diversification in East Africa and a later radiation in West/Central Africa. The West African situation was consistent with virus adaptation to savanna, forest and other ecological conditions. In contrast East Africa, as exemplified by the Tanzanian situation, with numerous physical barriers (mountain chains, sea channel, lakes), suggested that RYMV strains resulted from divergence under isolated conditions. For RYMV and for two other viruses, phylogenetic relationships were established between isolates from Madagascar and isolates from the Lake Victoria region.

Genetic diversity and population structure of rice stripe virus in China

“…the NS3 and N genes on RNA 3, and the NCP and NSvc4 genes on RNA 4, are almost identical (Table 4). This suggests that the single (Fraile et al, 1997) and molecular phylogeny (Abubakar et al, 2003). In this paper, we applied a distance-based NJ method to construct the phylogenetic trees of RSV isolates collected from different areas in China during 1997China during -2004.…”

Pathogenic Variation and Occurrence of Multiple Resistance-Breaking <i>Rice yellow mottle virus</i> Strains in Tanzania

“…Diverse groups of Rice yellow mottle virus strains are widely distributed in Tanzania [14] [15] [16] [17]. The strain S5 is restricted in Morogoro region, while S4 and S6 are widely spread throughout the country [14] [16].…”

“…The strain S5 is restricted in Morogoro region, while S4 and S6 are widely spread throughout the country [14] [16]. Rice (Oryza sativa L.) is one of the major staple foods ranking second after wheat worldwide [18].…”

Immunocapture and simple-direct-tube-reverse transcriptase polymerase chain reaction (RT-PCR) for detection of Rice yellow mottle virus

“…Strains S1, S2 and S3 have been reported to exist in West Africa with latitudes and longitudes between 4°N and 28°N and 15°E and 16°W, respectively. Strains S4, S5 and S6 are reported to dominate in East Africa which lies between latitudes 23°N and 12°S and longitudes 22°E and 51°E (Fargette et al, 2002;Abubakar et al, 2003;Banwo et al, 2004;Kanyeka et al, 2007).…”