The complete nucleotide sequence and genomic characterization of tropical soda apple mosaic virus

Fillmer, Kornelia; Adkins, Scott; Pongam, Patchara; D’Elia, Tom

doi:10.1007/s00705-016-2888-6

Cited by 6 publications

(4 citation statements)

References 8 publications

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“…Interestingly, this is the first work that reports the presence of TSMAV in humans. This virus was described about a decade ago 14 , and its complete genome sequence was reported only recently 15 , what probably explains the previous lack of description of this virus in human feces. This is relevant considering that the diversity of plant viruses has been poorly studied 1 , 2 , suggesting the possibility that additional, and so far undetected plant viruses may be commonly circulating in the human gut.…”

Section: Discussionmentioning

confidence: 99%

Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life

Aguado-García

Taboada

Morán

et al. 2020

Sci Rep

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Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant’s immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.

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Section: Discussionmentioning

confidence: 99%

Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life

Aguado-García

Taboada

Morán

et al. 2020

Sci Rep

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“…Tropical soda apple is naturally infected by tobamoviruses and members of several other families of agriculturally important viruses and may facilitate virus dissemination. Tobamoviruses are excellent for introducing the principles of phylogenetics to students because three major phylogenetic groups naturally form based on the host plant family infected (Solanaceae, Cucurbitaceae, or Brassicaceae) ( 6 , 10 ). Six single tobamovirus species branches also form, again based on host plant family.…”

Section: Methodsmentioning

confidence: 99%

“…Based on this analysis, students will recognize that the species form three major groups and six single species branches based on the host family these viruses infect. The phylogenetic analysis will place TSAMV with Pepper mild mottle virus (PMMoV) within the Solanaceae group ( 10 ). Students can then be directed to predict other host plants that TSAMV may potentially infect.…”

Section: Methodsmentioning

confidence: 99%

“…Several extensions to this activity emerge once the basic processes of multiple sequence alignments and phylogenetics are understood. Students can use the genome accession numbers in Appendix 2 to collect complete genome sequences, or amino acid sequences for MP or CP, to generate a phylogenetic tree and compare the results with their replicase tree and literature results ( 6 , 8 , 10 ).…”

Section: Methodsmentioning

confidence: 99%

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Using Tobamoviruses for Phylogenetic Instruction in Undergraduate Biology Courses

Fillmer

Adkins

Pongam

et al. 2018

J Microbiol Biol Educ.

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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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Solanum viarum (Tropical soda apple)

Sastry¹,

Mandal²,

Scott³

et al. 2019

Encyclopedia of Plant Viruses and Viroids

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The complete nucleotide sequence and genomic characterization of tropical soda apple mosaic virus

Cited by 6 publications

References 8 publications

Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life

Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life

Using Tobamoviruses for Phylogenetic Instruction in Undergraduate Biology Courses

Solanum viarum (Tropical soda apple)

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