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

Cockroaches Probably Cleaned Up after Dinosaurs

Dinosaurs undoubtedly produced huge quantities of excrements. But who cleaned up after them? Dung beetles and flies with rapid development were rare during most of the Mesozoic. Candidates for these duties are extinct cockroaches (Blattulidae), whose temporal range is associated with herbivorous dinosaurs. An opportunity to test this hypothesis arises from coprolites to some extent extruded from an immature cockroach preserved in the amber of Lebanon, studied using synchrotron X-ray microtomography. 1.06% of their volume is filled by particles of wood with smooth edges, in which size distribution directly supports their external pre-digestion. Because fungal pre-processing can be excluded based on the presence of large particles (combined with small total amount of wood) and absence of damages on wood, the likely source of wood are herbivore feces. Smaller particles were broken down biochemically in the cockroach hind gut, which indicates that the recent lignin-decomposing termite and cockroach endosymbionts might have been transferred to the cockroach gut upon feeding on dinosaur feces

An unprecedented Dianin clathrate structure with Z ' (host) = 16

The structure of the iso-propanol clathrate of 4-p-hydroxyphenyl 2,2,4-trimethylthiachroman, the direct thia- analogue of Dianin's compound, has been studied by single-crystal X-ray diffraction as a function of temperature from 371 K down to 90 K. The standard Dianin unit cell, observed at high temperature, undergoes two sequential commensurate thermal phase transformations which results at low temperature in a unit cell with 16 times the original volume and with Z'(host) = 16 and Z = 288, the space group R-3 being retained. This ultimate unit cell with a quadrupled a-axis has a = 111.7910(5)Å and c = 10.8568(1)Å and the crystal packing now features not only the prototypal [OH]6 hexamer host unit but also novel hydrogen-bonded octameric host-guest units with respective symmetries Ci and C1. In addition it has been established that the corresponding achiral selena-Dianin‘s clathrate and the polar chiral quasiracemic iso-propanol clathrate, space group R3, formed from R-Dianin's and S-Thia-Dianin's components also exhibit novel related temperature-dependant behaviour.Financial support from the Malaysia HIR MOHE, Grant No:F000009-21001 is gratefully acknowledged. We also wish to thank Dr Alex. R. Eberlin, Johnson-Matthey (Pharmorphix), Cambridge (UK), for assistance with the DSC experiments

Physical mapping of ribosomal DNA and genome size in diploid and polyploid North African Calligonum species (Polygonaceae)

38 p., tablas, gráf.Most Calligonum species are desert plants, characteristic of the Saharan bioclimatic region. All species karyologically analyzed until present have the basic chromosome number x = 9 and comprise diploids, triploids and tetraploids. The Tunisian flora comprises diploid Calligonum arich and C. azel, of restricted distribution, and the tetraploid C. comosum with wider distribution. Analyses of their karyotypes and polyploidisation-linked rDNA changes by orcein staining, fluorochrome banding with chromomycin A3 and fluorescent in situ hybridisation with 5S and 26S ribosomal DNA probes have been performed. We report the chromosome number for Calligonum arich (2n = 18) as well as the diploid level for C. comosum for the first time. Chromosome counts have also verified the earlier described tetraploid cytotype (2n = 36) of C. comosum. A general pattern of six GC-rich bands as well as two 35S sites and four 5S sites is described for Calligonum species at the diploid level although there is intraspecific variation regarding the site number in a second type of C. comosum, with one pair of 35S rDNA sites and two pairs of 5S rDNA sites. The tetraploid cytotype of C. comosum has undergone locus loss and genome downsizing. Genome size assessments confirmed previous data. Nonetheless, statistically significant differences were found depending on the type of tissue used for estimation. Measurements from seeds had always larger values than from leaves. The presence of cytosolic compounds in leaves, interfering with DNA staining, is discussed as a possible cause of the differences.This work was supported by the Dirección General de Investigación Científica y Técnica, government of Spain (CGL2010-22234-C02-01/BOS and CGL2010-22234-C02-02/BOS) and the Generalitat de Catalunya, government of Catalonia (‘‘Ajuts a grups de recerca consolidats’’, 2009SGR0439). SG and OH benefitted from Juan de la Cierva postdoctoral contracts of the Ministry of Economy and Competitiveness, government of Spain.Peer reviewe