Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

<p>Abstract</p> <p>Background</p> <p>Flax (<it>Linum usitatissimum </it>L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.</p> <p>Results</p> <p>The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.</p> <p>Conclusion</p> <p>The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.</p

Direct experimental evidence of tunable charge transfer at the LaNiO3/CaMnO3 ferromagnetic interface

Interfacial charge transfer in oxide heterostructures gives rise to a rich variety of electronic and magnetic phenomena. Designing heterostructures where one of the thin-film components exhibits a metal-insulator transition opens a promising avenue for controlling such phenomena both statically and dynamically. In this work, we utilize a combination of depth-resolved soft x-ray standing-wave and hard x-ray photoelectron spectroscopies in conjunction with polarization-dependent x-ray absorption spectroscopy to investigate the effects of the metal-insulator transition in LaNiO3 on the electronic and magnetic states at the LaNiO3/CaMnO3 interface. We report a direct observation of the reduced effective valence state of the interfacial Mn cations in the metallic superlattice with an above-critical LaNiO3 thickness (6 unit cells, u.c.) facilitated by the charge transfer of itinerant Ni3deg electrons into the interfacial CaMnO3 layer. Conversely, in an insulating superlattice with a below-critical LaNiO3 thickness of 2u.c., a homogeneous effective valence state of Mn is observed throughout the CaMnO3 layers due to the blockage of charge transfer across the interface. The ability to switch and tune interfacial charge transfer enables precise control of the emergent ferromagnetic state at the LaNiO3/CaMnO3 interface and, thus, has far-reaching consequences on the future strategies for the design of next-generation spintronic devices