The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence

Abstract

The complete genome sequence for an isolate of the Ugandan and Tanzanian strain types of Cassava brown streak virus have been determined using the novel approach of non-directed next generation sequencing. Comparison of the genome sequences revealed that CBSV is highly heterogeneous at the isolate level as well as the strain level. The isolate of the Ugandan strain was found to have a genome 9,070 nucleotides long coding for a polypeptide with 2,902 amino acid residues. The isolate of the Tanzanian strain was 9,008 nucleotides long and coded for a polypeptide with 2,916 amino acid residues. Nucleotide identity between the isolates across the genome was 76%, with protein encoding regions 57-77% and individual proteins had 65-91% amino acid similarity. In addition between the two strains four protein products (PIPO, CI, NIa-Vpg and coat protein) varied in size and an unusual HAM1-like protein, whilst of identical nucleotide length, was found to have the lowest homology. The implication of diversity of CBSV is discussed in the context of speciation, evolution, development of diagnostics, and breeding for resistance.

Evolution of cassava brown streak disease-associated viruses

“…The results of this study reveal wide occurrence of UCBSV in Ugandan highland and Kenyan lowland areas and are supported by recent reports, indicating that CBSD is associated with two viruses and not only CBSV known previously in the lowland areas (Alicai et al, 2007;Mbanzibwa et al, 2009a, b;Monger et al, 2010;Winter et al, 2010). The two viruses belong to the genus Ipomovirus (Winter et al, 2010) but are distinguished readily based on their whole-genome sequence divergence and less than 73 % nt sequence identity of the CP-encoding sequences.…”

“…1). The genome structures of CBSV and UCBSV are similar, but they differ from other ipomoviruses (Mbanzibwa et al, 2009a;Monger et al, 2010;Winter et al, 2010). CBSV and UCSBV encode a single P1 proteinase that is homologous to one of the two P1 proteinases encoded by Cucumber vein yellowing virus and Squash vein yellowing virus.…”

Characterization of Brown Streak Virus–Resistant Cassava

“…Sequencing efforts of CBSD infected cassava samples from different regions in East Africa led to the identification of two viral species (Mbanzibwa et al, 2009b;Monger et al, 2010;Winter et al, 2010;Ndunguru et al, 2015) now referred to as Cassava brown streak virus (CBSV), and Ugandan cassava brown streak virus (UCBSV). Despite their initial identification from distinct geographical zones, co-occurrence of CBSV and UCBSV has been reported and recent outbreaks of CBSD are not uniquely associated with a particular virus species Mbanzibwa et al, 2011a).…”

Cassava brown streak disease: a threat to food security in Africa

“…With advances in sequencing technologies, hitherto unknown viruses are now being identified by deep sequencing of RNA extracts from virus-infected plants (Kreuze et al, 2009). This approach has also been used for diagnosis of CBSVs (Monger et al, 2010).…”

“…To date, a total of 12 complete genome sequences of CBSV and UCBSV have been published, which cluster into two distinct phylogenetic groups (Fig. 2d) (Mbanzibwa et al, 2009a(Mbanzibwa et al, , 2011bMonger et al, 2010;Winter et al, 2010). The complete genomes of CBSV and UCBSV (four and eight isolates, respectively) show an identity of 69.0-70.3 % and 73.6-74.4 % at the nucleotide and polyprotein amino acid sequence levels, respectively.…”