Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan

Pecan (Carya illinoinensis) is a tree nut crop of worldwide economic importance that is rich in health-promoting factors. However, pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases. Here, we report a high-quality, chromosome-scale genome assembly of the controlled-cross pecan cultivar 'Pawnee' constructed by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry. The two paleo-subgenomes differ in size and protein-coding gene sets. They exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/Copia and LTR/Gypsy), and expansions in transcription factor families (such as the extreme pecan-specific expansion in the far-red impaired response 1 family), which are likely to reflect the long evolutionary history of species in the Juglandaceae. A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes. Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scab-susceptible cultivars 'Excell' and 'Pawnee'. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

Identification and Characterization of a New Pecan [Carya illinoinensis (Wangenh.) K. Koch] Allergen, Car i 2

The 7S vicilin and 11S legumin seed storage globulins belong to the cupin protein superfamily and are major food allergens in many foods from the "big eight" food allergen groups. Here, for the first time, pecan vicilin was found to be a food allergen. Western blot experiments revealed that 30% of 27 sera used in this study and 24% of the sera from 25 patients with double-blind, placebo controlled clinical pecan allergy contained IgE antibodies specific to pecan vicilin. This allergen consists of a low-complexity region at its N-terminal and a structured domain at the C-terminal that contains two cupin motifs and forms homotrimers. The crystal structure of recombinant pecan vicilin was determined. The refined structure gave R/Rfree values of 0.218/0.262 for all data to 2.65 Å. There were two trimeric biological units in the crystallographic asymmetric unit. Pecan vicilin is also a copper protein. These data may facilitate the understanding of the nutritional value and the allergenicity relevance of the copper binding property of seed storage proteins in tree nuts.

Cloning and characterization of an 11S legumin, Car i 4, a major allergen in pecan

Among tree nut allergens, pecan allergens remain to be identified and characterized. The objective was to demonstrate the IgE-binding ability of pecan 11S legumin and characterize its sequential IgE-binding epitopes. The 11S legumin gene was amplified from a pecan cDNA library and expressed as a fusion protein in Escherichia coli. The native 11S legumin in pecan extract was identified by mass spectrometry/mass spectrometry (MS/MS). Sequential epitopes were determined by probing the overlapping peptides with three serum pools prepared from different patients' sera. A three-dimensional model was generated using almond legumin as a template and compared with known sequential epitopes on other allergenic tree nut homologues. Of 28 patients tested by dot blot, 16 (57%) bound to 11S legumin, designated Car i 4. MS/MS sequencing of native 11S legumin identified 33 kDa acidic and 20-22 kDa basic subunits. Both pecan and walnut seed protein extracts inhibited IgE binding to recombinant Car i 4, suggesting cross-reactivity with Jug r 4. Sequential epitope mapping results of Car i 4 revealed weak, moderate, and strong reactivity of serum pools against 10, 5, and 4 peptides, respectively. Seven peptides were recognized by all three serum pools, of which two were strongly reactive. The strongly reactive peptides were located in three discrete regions of the Car i 4 acidic subunit sequence (residues 118-132, 208-219, and 238-249). Homology modeling of Car i 4 revealed significant overlapping regions shared in common with other tree nut legumins.

Cloning and characterization of 2S albumin, Car i 1, a major allergen in pecan

Although pecans are associated with IgE-mediated food allergies, the allergens responsible remain to be identified and characterized. The 2S albumin gene was amplified from the pecan cDNA library. Dot-blots were used to screen the recombinant protein with pecan allergic patients' serum. The affinity purified native protein was analyzed by Edman sequencing and mass spectrometry/mass spectrometry (MS/MS) analysis. Cross-reactivity with walnut was determined by inhibition enzyme-linked immunosorbent assay (ELISA). Sequential epitopes were determined by probing the overlapping peptides with three different patients' serum pool. The 3-dimensional homology model was generated, and the locations of the pecan epitopes were compared with those of known sequential epitopes on other allergenic tree nut homologues. Of 28 patients tested by dot-blot, 22 (79%) bound to 2S albumin, designated as Car i 1. Edman sequencing and the MS/MS sequencing of native 2S albumin confirmed the identity of recombinant (r) Car i 1. Both pecan and walnut protein extracts inhibited the IgE-binding to rCar i 1. Sequential epitope mapping indicated weak, moderate, and strong reactivity against 12, 7, and 5 peptides, respectively. Of the 11 peptides recognized by all serum pools, 5 peptides were strongly reactive and located in 3 discrete regions of the Car i 1 (amino acids 43-57, 67-78, and 106-120). Three-dimensional modeling revealed IgE-reactive epitopes to be solvent accessible and share significant homology with other tree nuts providing a possible basis for previously observed cross-reactivity.

Airborne pollen of Carya, Celtis, Cupressus, Fraxinus and Pinus in the metropolitan area of Monterrey Nuevo Leon, Mexico

The concentration of pollen grains in the atmosphere over the metropolitan area of Monterrey, Nuevo Leon, Mexico, was analyzed throughout a year from March 2003-February 2004, focused on the genus Carya, Celtis, Cupressus, Fraxinus and Pinus owing to their interest as etiological pollinosis agents in diverse regions of the world. A 7-day Hirst type volumetric spore and pollen trap was located on a building roof of the city at 15 m from ground level for continuous sampling. The total quantity of pollen recorded for the study period was 21,083 grains/m(3), corresponding to 49.75 % of the taxa of interest. February and March were the months with higher pollen amounts in the air with 7,525 and 2,781 grains/m(3), respectively, and amounted to 49 % of total year through pollen. Fraxinus was the genus which contributed to the largest amount of pollen with 28 % of total grains (5,935 grains/m(3)) followed by Cupressus with 13 % (2,742 grains/ m(3)). Celtis, Pinus and Carya contributed with 5.3 % , 2.7 % , and 0.6 % of total pollen, respectively. These results indicate that Fraxinus and Cupressus are present in the area in sufficient quantity to indicate likely involvement in the origin of allergic disorders in the human population.

Biochemical composition and immunological comparison of select pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars

On an edible portion basis, pecan moisture, protein, lipid, total soluble sugars, and ash contents ranged from 2.1% to 6.4%, 6.0% to 11.3%, 65.9% to 78.0%, 3.3% to 5.3%, and 1.2% to 1.8%, respectively. With the exception of a high tannin (2.7%) Texas seedling, pecan tannin content was in a narrow range (0.6-1.85%). Unsaturated fatty acids (>90%) dominated pecan lipid composition with oleic (52.52-74.09%) and linoleic (17.69-37.52%) acids as the predominant unsaturated fatty acids. Location significantly influenced pecan biochemical composition. Pecan lipid content was negatively correlated with protein (r = -0.663) and total sugar (r = -0.625). Among the samples tested using SDS-PAGE a common pattern, with minor differences, in subunit polypeptide profiles was revealed. Rabbit polyclonal antibody-based immunoblotting experiments (Western blot) also illustrated the similarity in polypeptide profiles with respect to immunoreactivity. All tested cultivars registered similar immunoreactivity when their protein extracts (each at 1 mg/mL) were assessed using inhibition ELISAs (mean +/- standard deviation = 0.89 +/- 0.20; n = 27) with the USDA "Desirable" cultivar as the reference standard (immunoreactivity designated as 1.0).

Antigenic stability of pecan [Carya illinoinensis (Wangenh.) K. Koch] proteins: effects of thermal treatments and in vitro digestion

Rabbit polyclonal antibody-based inhibition ELISA as well as immunoblotting analyses of proteins extracted from variously processed pecans (cv. Desirable) indicate that pecan proteins are antigenically stable. Pecan antigens were more sensitive to moist heat than dry heat processing treatments. SDS-PAGE and immunoblotting analysis of the native and heat-denatured proteins that were previously subjected to in vitro simulated gastric fluid digestions indicate that stable antigenic peptides were produced. Both enzyme-to-substrate ratio and digestion time were influential in determining the stability of pecan polypeptides. The stable antigenic polypeptides may serve as useful markers in developing assays suitable for the detection of trace amounts of pecans in foods.