Abstract
Cassava is a major staple food for 800 million people. Cassava brown streak disease (CBSD), is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is suppressing cassava yields in East Africa at an alarming rate. Previous studies have documented CBSV is more devastating than UCBSV. This is because CBSV is harder to breed resistance for, causes more infections and yield losses in cassava, and its species delimitation is more challenging. We set out to characterize the CBSV and UCBSV whole genomes from the 26 previously published genomes and three new from Uganda, using NGS data with the goal of uncovering genetic patterns that explain the observed biological differences. In this paper, we report phylogenetic relationships, rates of synonymous and non-synonymous substitutions, and whole genome-based evolutionary rates for CBSV and UCBSV. Using the whole genome sequences we produced the first coalescent based species tree estimation for CBSV and UCBSV which supports previously published studies pointing to multiple species of both CBSV and UCBSV. This new species framework led to the finding that CBSV has a faster rate of evolution when compared with UCBSV. The genes responsible for CBSV’s rapid rate of evolution are NIa, 6K2, NIb and P1. Furthermore, we have discovered that for CBSV, rates of nonsynonomous substitutions are more predominant than synonymous substitution and occur across the entire genome. All comparative analyses between CBSV and UCBSV presented suggests CBSV is outsmarting the cassava immune system, thus is more devastating and harder to control.
