Here, we analyzed the effects on Capsicum annuum plants of Trichoderma atroviride P. Karst strains altered in the expression of SWOLLENIN (SWO1), a protein with amorphogenic activity on plant cell wall components. Strains of T. atroviride that overexpressed the Taswo1 gene were constructed as well as deletion mutants. A novel, cheap and accurate method for assessing root colonization was developed. Colonization assays showed that the Taswo1 overexpressing strains invaded the host root better than the WT, resulting in a stronger plant growth-promoting effect. The expression of plant defense marker genes for both the systemic acquired resistance and induced systemic resistance pathways was enhanced in plants inoculated with Taswo1 overexpressing strains, while inoculation with deletion mutant strains resulted in a similar level of expression to that observed upon inoculation with the wild-type strain. Response to pathogen infection was also enhanced in the plants inoculated with the Taswo1 overexpressing strains, and surprisingly, an intermediate level of protection was achieved with the mutant strains. Tolerance to abiotic stresses was also higher in plants inoculated with the Taswo1 overexpressing strains but was similar in plants inoculated with the wild-type or the mutant strains. Compatible osmolyte production in drought conditions was studied. This study may contribute to improving Trichoderma biocontrol and biofertilization abilities.

The negative effects of climate change impact both farmers and consumers. This is exemplified in coffee, one of the most widely consumed beverages in the world. Yield loss in high-quality Coffea arabica L., due to the spread of coffee leaf rust (Hemileia vastatrix), results in lower income for subsistence farmers and volatile prices in markets and cafes. Genetic improvement of crops is a proven approach to support sustainable production while mitigating the effects of biotic and abiotic stresses and simultaneously maintaining or improving quality. However, the improvement of many species, including coffee, is hindered by low genetic diversity. This can be overcome by inducing novel genetic variation via treatment of seeds or cells with mutagens. To evaluate this approach in coffee, mutant populations created by incubating seed or embryogenic calli with the chemical mutagens ethyl methanesulphonate or sodium azide were subject to reduced-representation DNA sequencing using the ddRADseq approach. More than 10,000 novel variants were recovered. Functional analysis revealed hundreds of sequence changes predicted to be deleterious for gene function. We discuss the challenges of unambiguously assigning these variants as being caused by the mutagenic treatment and describe purpose-built computational tools to facilitate the recovery of novel genetic variation from mutant plant populations.

A circular DNA enrichment sequencing (CIDER-Seq) approach identified a New World (NW) begomovirus–alphasatellite complex associated with a leaf curl disease of tomato from plants collected in Morelos, México. Using one of 21 samples showing virosis-associated symptoms, CIDER-Seq data revealed the presence of various NW begomovirus species, namely Begomovirus solanumaureivariati (tomato golden mottle virus: ToGMoV), Begomovirus solanumseveri (tomato severe leaf curl virus: ToSLCV), and Begomovirus solanumlapazense (tomato chino La Paz virus: ToChLPV). Additionally, the alphasatellites Whiflysatellite guatemalaense (whitefly-associated Guatemala alphasatellite 1: WfaGA1) and Clecrusatellite guatemalaense (whitefly-associated Guatemala alphasatellite 2: WfaGA2) were identified, demonstrating that begomoviruses can co-infect with alphasatellites; however, the pathogenic implications of the alphasatellite–helper begomovirus association remain incompletely understood. PCR-based detection and Sanger sequencing of circular viral genomes revealed a high frequency of detection of mixed infections comprising all components of the begomovirus–alphasatellite complex, confirming the reliability of the CIDER-Seq approach in producing high-fidelity sequences. Molecular and biological analysis revealed the complex adaptation to tomato, the monopartite nature of ToSLCV/ToChLPV species, and the ability of these begomovirus species to act as helper viruses. To the best of our knowledge, this is the first report of leaf curl disease of tomato associated with a begomovirus–alphasatellite complex in Mexico.