BackgroundAlthough draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology.FindingsHere we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome.ConclusionsOur results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.

A new source of resistance to the highly virulent and widespread biotype L of the Hessian fly, Mayetiola destructor (Say), was identified in an accession of tetraploid durum wheat, Triticum turgidum Desf., and was introgressed into hexaploid common wheat, Triticum aestivum L. Genetic analysis and deletion mapping revealed that the common wheat line contained a single locus for resistance, H31, residing at the terminus of chromosome 5BS. H31 is the first Hessian fly-resistance gene to be placed on 5BS, making it unique from all previously reported sources of resistance. AFLP analysis identified two markers linked to the resistance locus. These markers were converted to highly specific sequence-tagged site markers. The markers are being applied to the development of cultivars carrying multiple genes for resistance to Hessian fly biotype L in order to test gene pyramiding as a strategy for extending the durability of deployed resistance.

Through gene-for-gene interactions, wheat plants respond to specific biotypes of Hessian fly upon the initiation of first-instar larval feeding. Leaves of plants containing the H9 resistance gene responded to avirulent biotype L. larvae with rapid changes in the levels of several mRNA transcripts and initiation of an incompatible interaction. A low-copy gene, Hfr-1 (Hessian fly-response gene 1), responded with increased mRNA levels for two days before returning to preinfestation levels by day five. Hfr-1 mRNA was constitutively expressed in uninfested control plants as well as in plants infested with virulent larvae. The cDNA sequence was similar to a maize gene encoding a beta-glucosidase aggregating factor (BGAF), to jacalin-like mannose-binding lectins, and to several plant genes that respond to microbial infections. The potential roles of Hfr-1 in defending wheat against Hessian fly damage are discussed.

The hypoglycaemic activity of Opuntia lindheimeri Englem. was investigated in non-diabetic (control pigs) and streptozotocin-induced diabetic pigs using an enteral (oral) route of administration. Following the administration of O. lindheimeri extract (0, 250 or 500 mg/kg body weight), blood glucose concentrations in control pigs fluctuated around initial baseline concentrations, but were not consistently affected by either the dose of O. lindheimeri or by the time following administration. In contrast, administration of O. lindheimeri extract to STZ-treated pigs resulted in both a dose- (p < 0.001) and time-dependent (p < 0.001) decrease in blood glucose concentrations. The hypoglycaemic effect of the extract was apparent within 1 h of administration, with maximal effects occurring at 4 h after administration. These results confirm the hypoglycaemic effect of O. lindheimeri extract in a diabetic pig model. In addition, given the physiological similarities of the pig to humans, this model will be of tremendous use in assessing the long-term effects of Opuntia administration on the secondary problems associated with diabetes.