A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

BACKGROUND

Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation.

RESULTS

Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production.

CONCLUSIONS

Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

The influence of biomass on the toxicity of hydrophobic organic contaminants

Hydrophobic organic contaminants (HOCs) enter the marine environment through several means, including industrial, urban, and agricultural runoff, and accumulate in sediments. Methods for measurement of sediment toxicity include porewater tests using sea urchin (Arbacia punctulata) fertilization and embryological development assessments. Previous studies investigating sediments from Boston Harbor determined that significant binding of contaminants to organic matter led to insufficient evidence of the bioavailability of HOCs in porewater toxicity tests. It was hypothesized that excessive biomass in testing systems prevents a critical body residue of HOCs from forming, thus curbing toxic effects. In this study, the effect of biomass on the toxicity of phenanthrene (a polycyclic aromatic hydrocarbon) and lindane (an organochlorine pesticide) were assessed individually and combined in a mixture. The fertilization toxicity test for phenanthrene and mixture solutions containing both compounds revealed less biomass in the test vial caused higher toxicity levels, the fact of which was enhanced with increased hydrophobicity. The 50% inhibition concentration (IC(50)) of phenanthrene to sea urchin fertilization success in test vials with 50 eggs/mL (lowest biomass concentration tested) was 3.72 micromol/L, but in vials with 100 to 400 eggs/mL, the IC(50) was >4.12 micromol/L. Toxicity of several concentrations of the phenanthrene and lindane mixture to sea urchin fertilization success and embryological development was significantly higher at lower biomasses (50 and 100 eggs or embryos/mL) than with biomasses > or =200 eggs or embryos/mL. The results suggest that when testing environmental samples that may contain HOCs, lowering the biomass can help better estimate sediment toxicity using porewater tests.

Toxicity of phenanthrene and lindane mixtures to marine invertebrates

Surface waters near industrialized and agricultural areas are contaminated with hundreds of different pollutants from a variety of sources. Methods for measurement of sediment, surface water, and porewater toxicity in marine environments include the sea urchin (Arbacia punctulata) fertilization and embryological development tests and copepod (Schizopera knabeni) survival and hatching success assessment. The concentration addition model was applied to determine whether toxicity of two compounds, phenanthrene (polycyclic aromatic hydrocarbon) and lindane (organochlorine pesticide), when combined can be accurately assessed because of similar modes of action. Mixture analysis determined the sea urchin fertilization test to exhibit additivity (TU(mix) = 1.13), while the copepod test exhibited a synergistic effect (TU(mix) = 0.22). Mixture toxicity data for the sea urchin embryological test were not conclusive because of the lack of toxicity of the individual chemicals. The synergistic effect to copepods is a concern as it indicates that greater toxic effects may occur when the compounds are present in mixtures. Results from this research suggest that increased toxicity to some categories of organisms should be expected near agricultural and industrial areas where pesticides and other types of compounds may occur simultaneously.

Identification of a polymorphic ryanodine receptor gene from Heliothis virescens (Lepidoptera: noctuidae)

cDNAs encoding the C-terminal 1172 amino acids of a ryanodine receptor (RyR) from the lepidopteran pest Heliothis virescens (Hv-RyR) have been cloned and characterised. Sequence comparisons, organisational studies on corresponding genomic regions and a genetic segregation analysis provide evidence for two polymorphic alleles of the Hv-RyR locus. Comparison of the Hv-RyR C-terminal amino acid sequence with equivalent regions of other RyRs reveals a high level of overall amino acid homology (74% identity with D. melanogaster and between 47.9 and 50.1% with vertebrate isoforms). Homologies are however not uniformly distributed, though regions of high and low similarity are consistent with patterns in other RyR isoforms. The structural similarity of Hv-RyR with other RyRs is also indicated by comparison of hydropathy profiles and other previously described functional domains. Such results are consistent with this region of Hv-RyR containing the Ca(2+) channel itself and being intimately involved in RyR regulation. Potential uses of the cDNAs described in the discovery and development of novel ryanodine like insecticides are discussed.

Chloride binding in the stroma of cultured human corneas

In the ox cornea, more than half of the non-diffusible, matrix negative charge is derived from the binding of free chloride ions. Because the magnitude of the net matrix charge is the dominant factor which determines the degree of stromal swelling, we investigated whether this phenomenon, stromal chloride binding, also occurs in human corneal stroma. Intrastromal ion concentrations were measured with radio-isotopes when human (outdated Eye Bank) corneas or (fresh) bovine corneas, physically clamped to maintain a constant hydration, were incubated in buffered 154 mM NaCl. The intrastromal chloride ion concentration was compared to the normalized concentrations of trace quantities of radio-labelled acetate and lactate ions. For human corneas, the intrastromal chloride ion concentration was found to be significantly higher (P < 0.001, t-test) than the normalized concentrations of both acetate and lactate ([Cl]i = 142.5 +/- 0.9 mM, (n = 9); [acetate]i = 131.2 +/- 1.2 mM, (n = 8); [lactate]i = 131.9 +/- 1.5 mM, (n = 5); all values are mean +/- S.E.M.). The sodium ion concentration was elevated ([Na]i = 176.0 +/- 1.8 mM, (n = 9)). These results demonstrate that chloride binding occurs to a significant extent in cultured human corneal stroma and suggest that chloride binding may be evident in the native human cornea.

Sudden death in squash players

A series of thirty sudden deaths (twenty-nine men, one woman) associated with squash playing is described. The subjects' mean age was 46.7 +/- SD 9.58 years (range 22-66). Necropsy results were available for twenty-seven subjects. Significant coronary heart disease (CHD) was found in twenty-three, valvular heart disease in three, and hypertrophic obstructive cardiomyopathy in one, and cardiac arrhythmia, in the absence of other pathology, was thought to have preceded death in two. One subject died from intracerebral haemorrhage. Twenty-two had reported prodromal symptoms, and of those with CHD, sixteen had had at least one identifiable CHD risk factor. Twelve subjects had been known by their family physician to have a medical disorder related to the cardiovascular system.

Q fever in an urban area

In the summer of 1981 29 patients living in Gwent, South Wales, had Q fever; 20 were diagnosed by routine clinical and laboratory services and 9 were discovered by active case-finding. The date of onset of symptoms spanned a 2-month period. The peak incidence was at the end of June. A case-control study showed an association with one area on the outskirts of Newport. Most patients had no direct contact with farms of farm animals and a common source of infection could not be identified. The most likely explanation of the outbreak was that farm vehicles had disseminated contaminated straw, manure, or dust in the area of Newport adjacent to farmland.

Influenza vaccination and mortality from bronchopneumonia in the elderly

In a three-year influenza vaccination programme carried out among elderly patients these were found to have a lower haemagglutination-inhibiting antibody level and a poorer serological response to vaccination than younger persons in the same city. Although there was little difference in overall respiratory illness between the vaccinated and unvaccinated groups until the third year of observation, those who received vaccine showed a substantially smaller incidence of bronchopneumonia and a significantly lower mortality than those not so protected. The observations are believed to justify the giving of influenza vaccine in this age-group.

Herpes simplex encephalitis treated with intravenous idoxuridine

Images