Phylogenetic analyses of peanut resistance gene candidates and screening of different genotypes for polymorphic markers

AbstractThe nucleotide-binding-site-leucine-rich-repeat (NBS–LRR)-encoding gene family has attracted much research interest because approximately 75% of the plant disease resistance genes that have been cloned to date are from this gene family. Here, we describe a collection of peanut NBS–LRR resistance gene candidates (RGCs) isolated from peanut (Arachis) species by mining Gene Bank data base. NBS–LRR sequences assembled into TIR-NBS-LRR (75.4%) and non-TIR-NBS-LRR (24.6%) subfamilies. Total of 20 distinct clades were identified and showed a high level of sequence divergence within TIR-NBS and non-TIR-NBS subfamilies. Thirty-four primer pairs were designed from these RGC sequences and used for screening different genotypes belonging to wild and cultivated peanuts. Therefore, peanut RGC identified in this study will provide useful tools for developing DNA markers and cloning the genes for resistance to different pathogens in peanut

Radiometric measurements of the microwave emissivity of foam

Includes bibliographical references.Radiometric measurements of the microwave emissivity of foam were conducted during May 2000 at the Naval Research Laboratory's Chesapeake Bay Detachment using radiometers operating at 10.8 and 36.5 GHz. Horizontal and vertical polarization measurements were performed at 36.5 GHz; horizontal, vertical, +45°, ­45°, left-circular, and right-circular polarization measurements were obtained at 10.8 GHz. These measurements were carried out over a range of incidence angles from 30° to 60°. Surface foam was generated by blowing compressed air through a matrix of gas-permeable tubing supported by an aluminum frame and floats. Video micrographs of the foam were used to measure bubble size distribution and foam layer thickness. A video camera was boresighted with the radiometers to determine the beam-fill fraction of the foam generator. Results show emissivities that were greater than 0.9 and approximately constant in value over the range of incidence angles for vertically polarized radiation at both 10.8 and 36.5 GHz, while emissivities of horizontally polarized radiation showed a gradual decrease in value as incidence angle increased. Emissivities at +45°, ­45°, left-circular, and right-circular polarizations were all very nearly equal to each other and were in turn approximately equal to the average values of the horizontal and vertical emissivities in each case.This work was sponsored by the Department of the Navy, Office of Naval Research under Award N0014-00-1-280 to the University of Massachusetts, Award N00014-00-0152 to the University of Washington, and Award N0001400WX21032 to the Naval Research Laboratory

Potential of herbariomics for studying repetitive DNA in angiosperms

Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data. Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g., different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space

The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae)

Background and Aims: We investigate whether changes in floral colour accompany polyploid and homoploid hybridisation, important processes in angiosperm evolution. Potentially, changes in floral colour can facilitate speciation through pollinator shifts. Methods: We examined spectral reflectance of corolla tissue from 60 Nicotiana (Solanaceae) accessions (41 taxa) based on spectral shape (corresponding to pigmentation) as well as bee and hummingbird colour perception to assess patterns of floral colour evolution. We compared polyploid and homoploid hybrid spectra to those of their progenitors to evaluate whether hybridisation has resulted in floral colour shifts. Key Results: Floral colour categories in Nicotiana seem to have arisen multiple times independently during the evolution of the genus. Polyploid and homoploid hybrids can display a floral colour: 1) intermediate between progenitors, 2) like one or other progenitor, or 3) a transgressive or divergent colour not present in either progenitor. Conclusions: Floral colour evolution in Nicotiana is weakly constrained by phylogeny, but colour shifts occur and are sometimes associated with allopolyploid or homoploid speciation. Transgressive floral colour in N. tabacum has arisen by inheritance of anthocyanin pigmentation from its paternal progenitor while having a plastid phenotype like its maternal progenitor. Potentially, floral colour evolution has been driven by, or resulted in, pollinator shifts

Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

BACKGROUND: The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. RESULTS: A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. CONCLUSION: EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species

Towards an 'average' version of the Birch and Swinnerton-Dyer Conjecture

The Birch and Swinnerton-Dyer conjecture states that the rank of the Mordell-Weil group of an elliptic curve E equals the order of vanishing at the central point of the associated L-function L(s,E). Previous investigations have focused on bounding how far we must go above the central point to be assured of finding a zero, bounding the rank of a fixed curve or on bounding the average rank in a family. Mestre showed the first zero occurs by O(1/loglog(N_E)), where N_E is the conductor of E, though we expect the correct scale to study the zeros near the central point is the significantly smaller 1/log(N_E). We significantly improve on Mestre's result by averaging over a one-parameter family of elliptic curves, obtaining non-trivial upper and lower bounds for the average number of normalized zeros in intervals on the order of 1/log(N_E) (which is the expected scale). Our results may be interpreted as providing further evidence in support of the Birch and Swinnerton-Dyer conjecture, as well as the Katz-Sarnak density conjecture from random matrix theory (as the number of zeros predicted by random matrix theory lies between our upper and lower bounds). These methods may be applied to additional families of L-functions.Comment: 20 pages, 2 figures, revised first draft (fixed some typos

Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry

Centerscope

Centerscope, formerly Scope, was published by the Boston University Medical Center "to communicate the concern of the Medical Center for the development and maintenance of improved health care in contemporary society.