An official website of the United States government
The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa – which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10^3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 – 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.
more »
« less
Alignments and ML trees of cassava brown streak virus and Ugandana cassava brown streak virus polyprotein nucleotide sequences
Alignments of full and nearly full polyprotein-length nucleotide sequences from GenBank for the two ipomoviruses that cause cassava brown streak disease, in fasta format. Separate alignments for 67 cassava brown streak virus sequences and 81 Ugandan cassava brown streak virus sequences are provided, as well as a combined alignment of 148 sequences. Alignments were created with MUSCLE and then modified by eye in AliView. Also, two tree files (in nexus) format are supplied, resulting from a maximum likelihood analysis with IQTree on each of the two single-species datasets. Support for nodes with aLRT and 100 actual bootstrap replicates are provided (aLRT/bootstrap).
more »
« less
- Award ID(s):
- 2308503
- PAR ID:
- 10530610
- Publisher / Repository:
- Zenodo
- Date Published:
- Subject(s) / Keyword(s):
- Molecular evolution RNA viruses cassava viruses
- Format(s):
- Medium: X
- Right(s):
- Creative Commons Attribution 4.0 International
- Institution:
- Rutgers, the State University of New Jersey
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Emerging plant viruses are one of the greatest problems facing crop production worldwide, and have severe consequences in the developing world where subsistence farming is a major source of food production, and knowledge and resources for management are limited. In Africa, evolution of two viral disease complexes, cassava mosaic begomoviruses (CMBs) (Geminiviridae) and cassava brown streak viruses (CBSVs) (Potyviridae), have resulted in severe pandemics that continue to spread and threaten cassava production. Identification of genetically diverse and rapidly evolving CMBs and CBSVs, extensive genetic variation in the vector, Bemisia tabaci (Hemiptera: Aleyrodidae), and numerous secondary endosymbiont profiles that influence vector phenotypes suggest that complex local and regional vector-virus plant-environment interactions may be driving the evolution and epidemiology of these viruses.more » « less
-
Duffy, Siobain (Ed.)Complete DNA-A sequences corresponding to East Aafrican cassava mosaic virus (EACMV), African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-Ug) were downloaded via the NCBI Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were manually adjusted with AliView (A. Larsson). Filesmore » « less
-
Societal Impact Statement Micronutrient deficiency or “hidden hunger” is estimated to affect two billion people worldwide and increasing the micronutrient concentration of food could play an important role in tackling this global challenge. Using a combination of imaging techniques and atomic absorption spectroscopy, we describe a link between root phenotype and micronutrient concentration in cassava, which could enable new phenotypic selection strategies for breeding. This approach could be used with existing breeding infrastructure to enhance the micronutrient concentration of cassava and hence, benefit the health of people, particularly in low‐income countries where cassava is consumed as a staple crop. SummaryCassava storage roots are a staple food in low‐income countries of South‐East Asia and sub‐Saharan Africa, where growth stunting is prevalent as a consequence of micronutrient deficiencies. We aim to link phenotypes of field‐grown cassava roots to micronutrient concentration in the edible storage roots as a simple way to improve phenotypic selection for nutritional value in cassava.We used existing and newly developed imaging techniques to quantify root phenotypes of the cassava root architecture over time and used flame atomic absorption spectroscopy to measure micronutrient concentration in storage roots. Both together allow the association of root phenotypes with micronutrient concentration in mature cassava roots.We show that early and late bulking genotypes in cassava exhibit distinct foraging behaviors that are associated with micronutrient concentration in the edible storage root. Our observations suggest that late bulking cassava is a key to provide sufficient micronutrients in the edible storage root.The association between root phenotype and micronutrient concentration with imaging techniques allows phenotypic selection for enhanced micronutrient concentration. Therefore, implementing image‐based phenotyping into cassava breeding programs in sub‐Saharan Africa and South‐East Asia could be an essential element to resolve micronutrient deficiencies that puts individuals at a higher risk of growth stunting.more » « less
-
null (Ed.)The complete genome of a new umbra-like virus from edible fig (Ficus carica) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is "fig umbra-like virus" (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus Umbravirus, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family Tombusviridae.more » « less
