College of Agriculture & Natural Resources

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Author: search.filters.author.Chaverri, Priscila

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    Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus
    (Springer Nature, 2018-11-26) Fonseca, Paula L. C.; Badotti, Fernanda; de Oliveira, Tatiana F. P.; Fonseca, Antônio; Vaz, Aline B. M.; Tomé, Luiz M. R.; Abrahão, Jônatas S.; Marques, João T.; Trindade, Giliane S.; Chaverri, Priscila; Aguiar, Eric R. G. R.; Góes-Neto, Aristóteles
    Hevea brasiliensis is an important commercial crop due to the high quality of the latex it produces; however, little is known about viral infections in this plant. The only virus described to infect H. brasiliensis until now is a Carlavirus, which was described more than 30 years ago. Virus-derived small interfering RNA (vsiRNAs) are the product of the plant’s antiviral defense triggered by dsRNA viral intermediates generated, during the replication cycle. These vsiRNAs are complementar to viral genomes and have been widely used to identify and characterize viruses in plants. In the present study, we investigated the virome of leaf and sapwood samples from native H. brasiliensis trees collected in two geographic areas in the Brazilian Amazon. Small RNA (sRNA) deep sequencing and bioinformatic tools were used to assembly, identify and characterize viral contigs. Subsequently, PCR amplification techniques were performed to experimentally verify the presence of the viral sequences. Finally, the phylogenetic relationship of the putative new virus with related viral genomes was analyzed. Our strategy allowed the identification of 32 contigs with high similarity to viral reference genomes, from which 23 exhibited homology to viruses of the Tymoviridae family. The reads showed a predominant size distribution at 21 nt derived from both strands, which was consistent with the vsiRNAs profile. The presence and genome position of the viral contigs were experimentally confirmed using droplet digital PCR amplifications. A 1913 aa long fragment was obtained and used to infer the phylogenetic relationship of the putative new virus, which indicated that it is taxonomically related to the Grapevine fleck virus, genus Maculavirus. The putative new virus was named Hevea brasiliensis virus (HBrV) in reference to its host. The methodological strategy applied here proved to be efficient in detecting and confirming the presence of new viral sequences on a ‘very difficult to manage’ sample. This is the second time that viral sequences, that could be ascribed as a putative novel virus, associated to the rubber tree has been identified.
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    Pseudocospeciation of the mycoparasite Cosmospora with their fungal hosts
    (John Wiley & Sons Ltd., 2016-01-03) Herrera, Cesar S.; Hirooka, Yuuri; Chaverri, Priscila
    Species of Cosmospora are parasites of other fungi (mycoparasites), including species belonging to the Xylariales. Based on prior taxonomic work, these fungi were determined to be highly host specific. We suspected that the association of Cosmospora and their hosts could not be a result of random chance, and tested the cospeciation of Cosmospora and the their hosts with contemporary methods (e.g., ParaFit, PACo, and Jane). The cophylogeny of Cosmospora and their hosts was found to be congruent, but only host-parasite links in more recent evolutionary lineages of the host were determined as coevolutionary. Reconciliation reconstructions determined at least five host-switch events early in the evolution of Cosmospora. Additionally, the rates of evolution between Cosmospora and their hosts were unequal. This pattern is more likely to be explained by pseudocospeciation (i.e., host switches followed by cospeciation), which also produces congruent cophylogenies.
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    Not as Ubiquitous as We Thought: Taxonomic Crypsis, Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)
    (PLoS One, 2013-10-18) Salgado-Salazar, Catalina; Rossman, Amy Y.; Chaverri, Priscila
    The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.