As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.de novo genome sequence | genome expansion | Solanaceae evolution

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

BackgroundGeminiviruses are a large and important family of plant viruses that infect a wide range of crops throughout the world. The Begomovirus genus contains species that are transmitted by whiteflies and are distributed worldwide causing disease on an array of horticultural crops. Symptom remission, in which newly developed leaves of systemically infected plants exhibit a reduction in symptom severity (recovery), has been observed on pepper (Capsicum annuum) plants infected with Pepper golden mosaic virus (PepGMV). Previous studies have shown that transcriptional and post-transcriptional gene silencing mechanisms are involved in the reduction of viral nucleic acid concentration in recovered tissue. In this study, we employed deep transcriptome sequencing methods to assess transcriptional variation in healthy (mock), symptomatic, and recovered pepper leaves following PepGMV infection.ResultsDifferential expression analyses of the pepper leaf transcriptome from symptomatic and recovered stages revealed a total of 309 differentially expressed genes between healthy (mock) and symptomatic or recovered tissues. Computational prediction of differential expression was validated using quantitative reverse-transcription PCR confirming the robustness of our bioinformatic methods. Within the set of differentially expressed genes associated with the recovery process were genes involved in defense responses including pathogenesis-related proteins, reactive oxygen species, systemic acquired resistance, jasmonic acid biosynthesis, and ethylene signaling. No major differences were found when compared the differentially expressed genes in symptomatic and recovered tissues. On the other hand, a set of genes with novel roles in defense responses was identified including genes involved in histone modification. This latter result suggested that post-transcriptional and transcriptional gene silencing may be one of the major mechanisms involved in the recovery process. Genes orthologous to the C. annuum proteins involved in the pepper-PepGMV recovery response were identified in both Solanum lycopersicum and Solanum tuberosum suggesting conservation of components of the viral recovery response in the Solanaceae.ConclusionThese data provide a valuable source of information for improving our understanding of the underlying molecular mechanisms by which pepper leaves become symptomless following infection with geminiviruses. The identification of orthologs for the majority of genes differentially expressed in recovered tissues in two major solanaceous crop species provides the basis for future comparative analyses of the viral recovery process across related taxa.

SUMMARYPepper is an economically important crop in many countries around the world but it is susceptible to many diseases. In Mexico, diseases caused by bipartite begomoviruses have emerged as important problems in pepper. Several control strategies have been explored wiht little success; most of them are based on the avoidance of virus transmission and the breeding for resistance. Abiotic inducers can act at various points in the signaling pathways involved in disease resistance, providing long-lasting, wide-spectrum resistance. Benzothiadiazole (BTH) shares the property of activating the systemic acquired resistance pathway downstream from the SA signaling. In this work, resistance to PepGMV infection was induced in pepper plants by activating the SA pathway using BTH treatment. The resistance was characterized by evaluating symptom appearance, virus accumulation and viral movement. Our results showed that BTH could be an attractive alternative to induce geminivirus resistance in pepper plants without a signifi cant damage of the fruit quality and productivity.

<p><strong>Background: </strong><em>Pepper huastecto yellow vein virus</em> (PHYVV) is one of the main viruses affecting pepper (<em>Capsicum</em> spp.) plants in Mexico.</p><p><strong>Question: </strong>Why there are no pepper resistant cultivars to PHYVV currently? Could it be due for the lack of new pepper resistant sources and knowledge about the heritability of the resistant trait?</p><p><strong>Study species: </strong><em>Capsicum annuum, Pepper huasteco yellow vein virus </em>and<em> Bemisia tabaci</em>.</p><p><strong>Study site: </strong>Culiacan<strong> </strong>Sinaloa, Mexico; January 2013 to August 2014.</p><p><strong>Methods: </strong>Two assays were performed in 2013 and 2014 with three resistant wild lines of <em>Capsicum annuum</em> in the S2 and S3 generation under greenhouse conditions to analyze the resistance to the <em>Pepper huasteco yellow vein virus</em> (PHYVV) and its heritability. Plants were inoculated with PHYVV through <em>Bemisia tabaci</em> G. and by grafting.</p><p><strong>Results: </strong>Line UAS12 showed a significantly higher proportion of resistant plants, longer incubation time, and less amount of viral DNA, followed by lines UAS13, UAS10 and the Maverick cultivar under both inoculation methods in both assays. Distribution of symptoms revealed a bimodal tendency in both assays. The novel gene "<em>CchGLP</em>" which confer resistance to PHYVV in pepper plants, was identified in the three lines evaluated on this study. Heritability of line UAS12 was of 0.35 and 0.26 in the insects and grafting inoculations, and of 0.58 and 0.10 in the first and second assays, respectively. Lines UAS13 and UAS10 showed close to zero heritability in the first and second assays with both inoculation methods.</p><strong>Conclusions: </strong>Line UAS12 is the most promising genetic resource for its high resistance and for showing heritability for the resistance trait. The intermediate resistance of lines UAS13 and UAS10 could be also useful for breeding programs. At least two genes are involved in the resistance trait to PHYVV. Part of the resistance shown in these lines may be due to the presence of the "<em>CchGLP</em>" gene. Line UAS12 count with variability for the resistant trait and can, therefore, be used to improve resistance and the other two lines possibly are stable as they did not show heritability.