Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.

Opuntioideae, composed of roughly 370 species, occur in almost every biome in the Americas, from seasonally dry tropical forests (SDTF) to high-elevation Andean grasslands, American deserts and temperate zones. The interrelationships among the three major clades of Opuntioideae (Cylindropuntieae, Opuntieae and Tephrocacteae) are not well resolved, and thus, the ancestral habitat, biogeographic history and evolution of morphological characters, such as large photosynthetic leaves and flattened stems, are poorly understood. To test their geographic origin and evolution of key morphological characters, we built the largest phylogenomic dataset for Cactaceae to date using 103 plastid genes of 107 taxa of Opuntioideae. The subfamily Opuntioideae likely evolved in South America in a combination of seasonally dry tropical forest (SDTF)/desert habitats. Opuntieae most likely evolved in South America in SDTF and, from there, moved into desert regions, Chaco and temperate/subtropical zones, while Tephrocacteae and Cylindropuntieae evolved in South America in desert regions and moved into SDTF, Chaco and temperate/subtropical zones. Analyses of morphological evolution suggest that, although large leaves are plesiomorphic in Opuntioideae, long-lived, photosynthetically active leaves in Cylindropuntieae and Tephrocacteae are homoplasious and do not represent retained plesiomorphy, as is often assumed. Flattened stems are synapomorphic for Opuntieae, possibly representing adaptation to competition for light resources in SDTF, their most likely ancestral area.

Resumo O Brasil é o país com a maior biodiversidade conhecida no mundo, mas sua flora alimentícia ainda carece de estudos. No presente trabalho, apresentamos um levantamento de plantas frutíferas nativas do estado do Rio Grande do Sul com base em consultas bibliográficas e experimentação de campo. Dados adicionais de cada espécie, como nome popular, forma biológica, distribuição geográfica, hábitat, fenologia, tamanho da fruta e forma de uso também são apresentados. Reportamos 213 espécies frutíferas nativas distribuídas em 48 famílias e 102 gêneros, sendo Myrtaceae a família com o maior número de espécies. A maioria das espécies é constituída por árvores que ocorrem em ambientes florestais, distribuídas ao longo de todo território do estado. Mais de 90% das frutas são para consumo in natura ou derivados, enquanto uma pequena parte é utilizada após processamento, e outra parte é utilizada como condimento. Cerca de 20% das espécies são apresentadas de maneira inédita como frutíferas. Ressalta-se a elevada riqueza de espécies frutíferas encontrada no estado e a importância da valorização da flora nativa alimentícia com potencial de uso sustentável, incrementando a fruticultura local e agregando valor à produção agrícola.

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.