Rita Cássia Pereira-Carvalho

Beans (Phaseolus vulgaris and P. lunatus) are the major hosts of bean golden mosaic begomovirus (BGMV). Robust taxonomic criteria were established for Begomovirus species demarcation. However, DNA–A identities among BGMV isolates display a continuous variation (89–100%), which conflicts with the current concept of a single viral species. The diversity of 146 Brazilian isolates designated in the GenBank as BGMV was assessed by comparing their complete DNA–A sequences. The isolates were clustered into four groups, being discriminated mainly by their original Fabaceae hosts. Additional Sequence Demarcation Tool analyses indicated that BGMV-related viruses comprise two clear-cut groups: isolates reported infecting mainly P. vulgaris (identities of 96–97% to the reference NC_004042 isolate) and a group associated with P. lunatus (identities of 89–91%). Moreover, we recognized a distinct set of genomic features in the iterons and Rep-associated protein motifs across these two diversity groups. The host prevalence and genomic differences suggest that most P. lunatus isolates are currently misclassified as BGMV strains, being more likely samples of a closely related (but distinct) Begomovirus species. Hence, the implications of this BGMV diversity should be taken into consideration by classical and biotech breeding programs aiming for large-spectrum viral resistance in Phaseolus species.

A new alphasatellite was discovered via high-throughput sequencing in mixed infections with five distinct tomato-infecting begomoviruses in central Brazil, and the presence of this alphasatellite in tomato leaf samples was confirmed by PCR and Sanger sequencing. It has a circular genome of 1,321 nucleotides with typical features of alphasatellites belonging to the subfamily Geminialphasatellitinae, including a replication-associated hairpin sequence (TAGTATTAC) and an open reading frame encoding a replication-associated protein. Pairwise sequence comparisons and phylogenetic analysis indicated that this alphasatellite represents a new species, with 69–77% sequence identity to other members of the genus Clecrusatellite. Tomato golden vein virus (TGVV) was the only begomovirus present in all six positive samples. However, it was not possible to determine which of these viruses can function as a helper virus for the alphasatellite. The species name "Clecrusatellite solanumbrasiliensis" is proposed to classify this alphasatellite associated with endemic Brazilian begomoviruses. To our knowledge, this is the first report of a tomato-associated alphasatellite in the New World.

Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (Geminiviridae). However, the range of DNA–A identity of isolates of these viruses (81–100%) is not in agreement with the current criteria for Begomovirus species demarcation (n = 47) comprises a wide range of strains (with a continuum variation of 88.8–100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90–100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as “true SiMMV”). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA–B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species.

The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central–West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty–1 or Ty–3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions.

The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.

Two novel tomato-infecting begomoviruses were discovered via high-throughput sequencing in Brazil. Both viruses were also Sanger-sequenced and displayed DNA–A components phylogenetically related to New World bipartite begomoviruses. The names tomato golden net virus (ToGNV) and tomato yellow net virus (ToYNV) were proposed. The majority of the New World begomoviruses has bipartite genomes. However, extensive analyses revealed that ToGNV and ToYNV have monopartite genomes, because no cognate DNA–B components were detected. Hence, they may comprise a unique group of monopartite New World begomoviruses, which have enormous biological, molecular, and plant breeding interest.

Eggplant (Solanum melongena L.) is an economically important vegetable crop in Brazil, especially in family-based farming. Eggplant hybrids ‘Ciça’ and ‘Napoli’ (≈ 400 plants) were detected exhibiti...