Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

BackgroundStrawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique.MethodsThe study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided.ResultsA total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed.ConclusionsFrom a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/2046-4053-4-9) contains supplementary material, which is available to authorized users.

BackgroundIn plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes.ResultsA physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes.ConclusionsS. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0645-8) contains supplementary material, which is available to authorized users.

The European hazelnut (Corylus avellana L.) is a monoeciuos tree and exhibits sporophytic self-incompatibility. Self-incompatibility is a genetic system that prevents the selffertilization allowing the pistil to reject the pollen of genetically close individuals. Selfincompatibility is controlled by a single multi-allelic locus, the S locus. Sporophytic self-incompatibility (SSI) has been reported in: Asteraceae, Betulaceae, Brassicaceae, Caryophillaceae, Convolvulaceae and Sterculiaceae. The involved molecular mechanisms are still partly unknown but in the Brassicaceae. Studies on gene regulation of fertility, pollination and fertilization in hazelnut are very few; so with this research we propose to contribute to the knowledge about the mechanism of sporophytic selfincompatibility in hazelnut. The Differential Display technique was applied for the study of the female determinant of selfincompatibility. Two developmental stages of styles/stygmas were compared: before emergence from the bud and at full bloom. The results allowed to isolate partial sequences that showed an interesting homology degree with transmembrane serine-threonine kinase receptor of Brassica oleracea. Believing that the female determinant of self-incompatibility in hazelnut is very likely a membrane receptor, the efforts for getting differentially expressed sequences of this type were increased. Primers were designed on conserved regions of serinethreonine kinase receptors. Four differentially expressed fragments were isolated from stigmas at full bloom: after blasting in TIGR and NCBI databases, one was homologous to a gene for a kinase receptor, three were homologous to kinase proteins. The isolated sequences are being studied to check their expression in different tissues and style developmental stages. INTRODUCTIONThe genus Corylus is a member of the Betulaceae family of the order Fagales and includes several species, among which the European hazelnut (Corylus avellana L.) provides the most important cultivated varieties. Corylus avellana L. is a wind-pollinated, monoeciuos species that exhibits sporophytic self-incompatibility (Thompson, 1979;Me et al., 1983;Zannini et al., 1983;Me et al., 2000). Cultivars thus need to be cross-pollinated by pollinizer trees planted in the orchard in order to ensure good nut set. In addition, the frequent cross-incompatibility between cultivars