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Characterization by Next Generation Sequencing Reveals the Molecular Mechanisms Driving the Faster Evolutionary rate of Cassava brown streak virus Compared with Ugandan cassava brown streak virus

Titus Alicai, Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Geoffrey Okao-Okuja, Resty Nanvubya, Lilliane Kiiza, Laura Kubatko, Monica A Kehoe, Laura M Boykin
doi: https://doi.org/10.1101/053546
Titus Alicai
1National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
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Joseph Ndunguru
2Mikocheni Agricultural Research Institute, Coca cola Road, Box 6226, Dar es Salaam, Tanzania
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Peter Sseruwagi
2Mikocheni Agricultural Research Institute, Coca cola Road, Box 6226, Dar es Salaam, Tanzania
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Fred Tairo
2Mikocheni Agricultural Research Institute, Coca cola Road, Box 6226, Dar es Salaam, Tanzania
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Geoffrey Okao-Okuja
1National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
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Resty Nanvubya
1National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
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Lilliane Kiiza
1National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
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Laura Kubatko
3The Ohio State University, 154W 12th Avenue, Columbus, Ohio 43210, USA
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Monica A Kehoe
4Crop Protection Branch, Department of Agriculture and Food, Western Australia, Bentley Delivery Centre, Perth, 6983, Western Australia, Australia
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Laura M Boykin
5The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology and School of Chemistry and Biochemistry, Crawley, Perth 6009, Western Australia, Australia
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  • For correspondence: laura.boykin@uwa.edu.au
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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.

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Posted May 16, 2016.
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Characterization by Next Generation Sequencing Reveals the Molecular Mechanisms Driving the Faster Evolutionary rate of Cassava brown streak virus Compared with Ugandan cassava brown streak virus
Titus Alicai, Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Geoffrey Okao-Okuja, Resty Nanvubya, Lilliane Kiiza, Laura Kubatko, Monica A Kehoe, Laura M Boykin
bioRxiv 053546; doi: https://doi.org/10.1101/053546
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Characterization by Next Generation Sequencing Reveals the Molecular Mechanisms Driving the Faster Evolutionary rate of Cassava brown streak virus Compared with Ugandan cassava brown streak virus
Titus Alicai, Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Geoffrey Okao-Okuja, Resty Nanvubya, Lilliane Kiiza, Laura Kubatko, Monica A Kehoe, Laura M Boykin
bioRxiv 053546; doi: https://doi.org/10.1101/053546

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