Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

The emergence of begomoviruses (whitefly-transmitted viruses classified in the genus Begomovirus, family Geminiviridae) in Brazil probably occurred by horizontal transfer from non-cultivated plants after the introduction of Bemisia tabaci MEAM1. The centre of diversity of Euphorbia heterophylla (Euphorbiaceae) is located in Brazil and Paraguay, where it is an invasive species in soybean and other crops. Reports of possible begomovirus infection of E. heterophylla in Brazil date back to the 1950s. In 2011, Euphorbia yellow mosaic virus (EuYMV) was described in symptomatic plants collected in the Brazilian state of Goiás. Here we assess the genetic variability and population structure of begomoviruses infecting E. heterophylla in samples collected throughout nine Brazilian states from 2009 to 2014. A total of 158 and 57 haplotypes were compared in DNA-A and DNA-B datasets, respectively. Analysis comparing population structure in a large sampled area enabled us to differentiate two subpopulations. Further, the application of discriminant analysis of principal components allowed the differentiation of six subpopulations according to sampling locations and in agreement with phylogenetic analysis. In general, negative selection was predominant in all six subpopulations. Interestingly, we were able to reconstruct the phylogeny based on the information from the 23 sites that contributed most to the geographical structure proposed, demonstrating that these polymorphisms hold supporting information to discriminate between subpopulations. These sites were mapped in the genome and compared at the level of amino acid changes, providing insights into how genetic drift and selection contribute to maintain the patterns of begomovirus population variability from a geographical structuring point of view.

Anthracnose, caused by Colletotrichum spp., is one of the major fungal diseases that affect Capsicum spp. and leads to severe crop losses. The aim of this study was to identify species within Colletotrichum that cause anthracnose in bell and hot pepper using phylogenetic and morphological criteria. Pathogenic isolates were obtained from bell and hot peppers exhibiting anthracnose symptoms and grown in the northeastern region of Brazil. These were initially identified based on the sequences of GAPDH, ACT, CAL, β-TUB genes and the ITS-rDNA region. Mycelial growth, coloration of the colony, size and shape of conidia and appressoria were determined for the selected isolates. It was concluded that five species: C. brevisporum, C. scovillei, C. siamense, C. tropicale and C. truncatum compose the species complex associated with anthracnose of Capsicum spp. in northeastern Brazil.

-Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants. The aim of this study was to further characterize the diversity of begomoviruses infecting weeds (mostly Sida spp.) in Brazil. Total DNA was extracted from weed samples collected in Viçosa (Minas Gerais state) and in some municipalities of Alagoas state in 2009 and 2010. Viral genomes were amplified by RCA, cloned and sequenced. A total of 26 DNA-A clones were obtained. Sequence analysis indicated the presence of 10 begomoviruses. All viral isolates from Blainvillea rhomboidea belonged to the same species, Blainvillea yellow spot virus (BlYSV ), thereby suggesting that BlYSV may be the only begomovirus present in this weed species. Four isolates represent new species, for which the following names are proposed: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) and Sida yellow mosaic Alagoas virus (SiYMAV). Recombination events were detected among the SiYBV isolates and in the SiYNV isolate. These results constitute further evidence of the high species diversity of begomoviruses in Sida spp. However, the role of this weed species as a source of begomoviruses infecting crop plants remains to be determined.Keywords: geminivirus, recombination, Blainvillea rhomboidea, Sida micrantha, Sida urens, Sida santaremnensis RESUMO -Begomovírus são vírus de DNA circular fita simples transmitidos por mosca branca, os quais são frequentemente associados com plantas daninhas. O objetivo deste trabalho foi caracterizar a diversidade de begomovírus infectando plantas daninhas (principalmente Sida spp.) no Brasil. DNA total foi extraído a partir de plantas daninhas coletadas em Viçosa (Minas Gerais) e em alguns municípios do estado de Alagoas em 2009 e 2010. Os genomas virais foram amplificados por RCA, clonados e sequenciados. Um total de 26 clones de DNA-A foram obtidos. A análise das sequências indicou a presença de dez diferentes begomovírus. Todos os isolados originários de Blainvillea rhomboidea pertencem a uma única espécie viral, Blainvillea yellow spot virus (BlYSV), sugerindo que o BlYSV pode ser o único begomovírus presente nesta espécie de planta invasora. Quatro isolados representam espécies novas, para as quais os seguintes nomes são propostos: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) e Sida yellow mosaic Alagoas virus (SiYMAV). Eventos de recombinação foram detectados entre isolados de SiYBV e no isolado de SiYNV. Estes resultados constituem uma evidência adicional da alta diversidade de espécies de begomovírus em Sida spp. Contudo, o possível papel dessas plantas daninhas como fonte de begomovírus para plantas cultivadas ainda permanece indeterminado.

The family Caulimoviridae comprises virus species that replicate by reverse transcription, and is composed by seven genera. Viruses classified within the genus Badnavirus are pathogens in economically important crops worldwide, and previous studies suggest a high genetic diversity in badnaviruses infecting cultivated hosts. To assess the genetic diversity of sugarcane-infecting badnaviruses, samples were obtained from a germplasm collection in Brazil in 2013. A total of 300 samples were collected, and PCR-analysis showed a badnavirus incidence level of 36 %. Partial sequences comprising the RT/RNaseH genomic region were obtained for 37 isolates. Sequence analysis showed the presence of at least six badnavirus species, with one being novel. The phylogenetic analysis showed that some sugarcane isolates are closely related to badnaviruses infecting banana (Musa spp.). KeywordsCaulimoviridae . Saccharum spp . Sugarcane bacilliform viruses The family Caulimoviridae comprises virus species that replicate by reverse transcription, and is composed of seven genera: Badnavirus, Caulimovirus, Cavemovirus, Petuvirus, Solendovirus, Soymovirus and Tungrovirus (Geering and Hull 2012). Viruses classified within the genus Badnavirus have bacilliform morphology, with particles measuring ca. 130×30 nm and containing a double-stranded DNA genome of 7.2-9.2 kb (Geering and Hull 2012). The demarcation of badnavirus species is based on host range, vector specificities and the determination of the nucleotide sequence of the RT/ RNaseH genomic region. The International Committee on Taxonomy of Viruses (ICTV) has established a species demarcation threshold of ≥80 % nucleotide identity for the RT/ RNaseH region (Geering and Hull 2012). Badnaviruses are transmitted in a semi-persistent manner by mealybugs (Geering and Hull 2012) and can infect a wide range of economically important crops including sugarcane (Saccharum spp.; Lockhart and Autrey 1988), banana (Musa spp.; Geering et al. 2000), yams (Dioscorea spp.; Phillips et al. 1999) and pineapple (Ananas comosus; Gambley et al. 2008).

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