Tomato mottle mosaic virus was recently reported from the United States following its original description from Mexico as a novel Tobamovirus species. We present the first complete genome sequence of a tomato mottle mosaic virus isolate from the United States.
We report the first complete genome sequence of tropical soda apple mosaic virus (TSAMV), a tobamovirus originally isolated from tropical soda apple (Solanum viarum) collected in Okeechobee, Florida. The complete genome of TSAMV is 6,350 nucleotides long and contains four open reading frames encoding the following proteins: i) 126-kDa methyltransferase/helicase (3354 nt), ii) 183-kDa polymerase (4839 nt), iii) movement protein (771 nt) and iv) coat protein (483 nt). The complete genome sequence of TSAMV shares 80.4 % nucleotide sequence identity with pepper mild mottle virus (PMMoV) and 71.2-74.2 % identity with other tobamoviruses naturally infecting members of the Solanaceae plant family. Phylogenetic analysis of the deduced amino acid sequences of the 126-kDa and 183-kDa proteins and the complete genome sequence place TSAMV in a subcluster with PMMoV within the Solanaceae-infecting subgroup of tobamoviruses.
Foliar symptoms suggestive of virus infection were observed on the ornamental plant hoya (Hoya spp.; commonly known as waxflower) in Florida. An agent that reacted with commercially available tobamovirus detection reagents was mechanically transmitted to Chenopodium quinoa and Nicotiana benthamiana. Rod-shaped particles ∼300 nm in length and typical of tobamoviruses were observed in partially purified virion preparations by electron microscopy. An experimental host range was determined by mechanical inoculation with virions, and systemic infections were observed in plants in the Asclepiadaceae, Apocynaceae, and Solanaceae families. Some species in the Solanaceae and Chenopodiaceae families allowed virus replication only in inoculated leaves, and were thus only local hosts for the virus. Tested plants in the Amaranthaceae, Apiaceae, Brassicaceae, Cucurbitaceae, Fabaceae, and Malvaceae did not support either local or systemic virus infection. The complete genome for the virus was sequenced and shown to have a typical tobamovirus organization. Comparisons of genome nucleotide sequence and individual gene deduced amino acid sequences indicate that it is a novel tobamovirus sharing the highest level of sequence identity with Streptocarpus flower break virus and members of the Brassicaceae-infecting subgroup of tobamoviruses. The virus, for which the name Hoya chlorotic spot virus (HoCSV) is proposed, was detected in multiple hoya plants from different locations in Florida.
Tomato mosaic virus was reported from jasmine in Florida. We present the first complete genome sequence of a tomato mosaic virus isolate from this woody perennial plant in the United States.
Microbial diversity and taxonomy instruction provide an ideal opportunity to introduce students to basic bioinformatics skills. There are many ways to illustrate evolutionary relationships between microorganisms using phylogenetic trees. Thought must be given to the method of presentation used in class because interpreting complex trees can be quite challenging for students. Here we present a simple activity that teaches the fundamental bioinformatics skills of multiple sequence alignments and phylogenetics by using Tropical soda apple mosaic virus and other tobamoviruses that produce trees that are easy to interpret. Tobamoviruses are important agricultural pathogens and have well defined phylogenetic groupings that correspond to the phylogenetic groupings of host plant families. This clear pattern illustrates the coevolution of the virus and host, and makes interpreting relationships based on these trees very straightforward. The organization of the trees also indicates related plants that a given virus may potentially infect, making this type of analysis useful for developing measures to limit spread and minimize economic impacts. The simplicity of the analysis, coupled with the real-world application in agricultural science, helps actively engage students in a topic that is challenging to learn. This activity is broadly adaptable, and can be introduced as a learning module in courses covering topics in microbiology, molecular biology, genetics and evolution. Completion of this activity provides students with key foundational skills for phylogenetic analysis and the confidence to utilize bioinformatics software.
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