Berries

The extraction buffer contained 300 mM Tris HCl (pH 8.0), 25 mM EDTA, 2 M NaCl, 2% CTAB, 2% PVPP, 0.05% spermidine trihydrochloride, and just prior to use, 2% β-mercaptoethanol. Tissue was ground to a fine powder in liquid nitrogen using a mortar and pestle. The powder was added to pre-warmed (65°C) extraction buffer at 20 ml/g of tissue and shaken vigorously. Since berries have higher water content than other grape tissues, a lower extraction buffer ratio of 10–15 ml/g weight was sufficient. Tubes were subsequently incubated in a 65°C water bath for 10 min and shaken every couple of min. Mixtures were extracted twice with equal volumes chloroform:isoamyl alcohol (24:1) then centrifuged at 3,500 × g for 15 min at 4°C. The aqueous layer was transferred to a new tube and centrifuged at 30,000 × g for 20 min at 4°C to remove any remaining insoluble material. This step proved more critical for root and flower tissues. To the supernatant, 0.1 vol 3 M NaOAc (pH 5.2) and 0.6 vol isopropanol were added, mixed, and then stored at -80°C for 30 min. Nucleic acid pellets (including any remaining carbohydrates) were collected by centrifugation at 3,500 × g for 30 min at 4°C. The pellet was dissolved in 1 ml TE (pH 7.5) and transferred to a microcentrifuge tube. To selectively precipitate the RNA, 0.3 vol of 8 M LiCl was added and the sample was stored overnight at 4°C. RNA was pelleted by centrifugation at 20,000 × g for 30 min at 4°C then washed with ice cold 70% EtOH, air dried, and dissolved in 50–150 μl DEPC-treated water.

The samples were classified into 24 different categories covering products from the plant kingdom, products from the animal kingdom and mixed food products. Information about sample processing (raw, cooked, dried etc), if any, was included, along with all sample specifications, i.e. product name, brand name, where the product/sample was procured and country of origin. The product information in the database was collected from the packing of the product, from supplier or purchaser. When this information was not available or the samples were handpicked, only country of origin is presented. Each sample is assigned to only one category. The classification was done according to information from the supplier or purchaser, or according to common traditional use of the food. Some foods may therefore be categorized otherwise in other food cultures. For products in the categories "Herbal/traditional plant medicine" and "Vitamin and dietary Supplements" some products may rightfully be classified as both an herbal medicine and a supplement, but are still assigned to only one category. All berries, fruits, and vegetables were fresh samples unless otherwise noted in the database. The Antioxidant Food Table contains 3139 samples. About 1300 of these samples have been published before [16 (link),17 (link),28 (link)] but for comparison and completeness we have included them in the present publication. All individual samples previously published are identified by a comment in the Antioxidant Food Table. The categories and products in the database are presented in alphabetic order. Information about brand names and product trademarks does not imply endorsement by the authors, and are reported as descriptive information for research applications only. The Antioxidant Food Table will in the future be available online as a searchable database. In addition to the products mentioned in this paper, other foods will in the future be analyzed and incorporated into the online version, which will be posted on the University of Oslo's web site.

In order to get specific markers for the alien chromosome, we screened 197 wheat group-7-specific microsatellite markers reported by Somers et al. (2004) (link) and 88 pairs of sequence-tagged sites-polymerase chain reaction (STS-PCR) primers on wheat group-7 chromosomes (Supplementary Table S1). At the two-leaf stage, 27 plants of T14-44 and 25 plants of T14-42 were collected and separately pooled for RNA isolation using a TRIzol reagent (Invitrogen^TM, Shanghai, China), followed by the treatment with DNase I (Invitrogen^TM, Shanghai, China). The samples were sequenced using the Illumina Hiseq2500 platform (Berry Genomics, Beijing, China) to generate 125 bp pair-end reads. The de novo assembly of clean reads was performed by using the software Trinity 2.1.1 (Haas et al., 2013 (link)). The expression level was calculated by mapping reads to the assembled transcripts employing Trinity scripts, RSEM, and edgeR (Haas et al., 2013 (link)). The TransDecoder software package (https://sourceforge.net/projects/transdecoder/) was used to predict the coding region for these transcripts. The transcripts were annotated in the Swiss-Prot database using Blastx. The transcripts expressed in T14-44 but not in T14-42 were extracted. Then, the transcripts annotated as Nucleotide Binding Site–Leucine Rich Repeat (NBS-LRR) protein and protein kinases were used to design primers using the software Primer 5.0 (PREMIER Biosoft, San Francisco, CA, USA).
The conditions of the polymerase chain reaction (PCR) were as follows: initial denaturation at 94°C for 4 min, followed by 35 cycles of 30 s at 94°C, 30 s for annealing at 55°C–60°C, 1 min for extension at 72°C, and a final extension at 72°C for 10 min. Amplified PCR products were separated on 8% non-denaturing polyacrylamide gels stained with silver at 200 V for 1 h and 1.5% agarose gels stained with ethidium bromide at 150 V for approximately 25 min. The D2000 Plus DNA Ladder (GenStar, Beijing, China) and the 100 bp DNA Ladder (TianGen Biotech Co, Beijing, China) were used for the DNA marker in non-denaturing polyacrylamide gel and agarose gel electrophoresis, respectively.

Nine-year-old blueberry (V. corymbosum “Duke”) plants collected from the small berry garden of the Fruit Tree Research Institute, Chinese Academy of Agricultural Sciences were used as experimental material. Experiments were conducted from March 2019 to February 2022 at the Ministry of Agriculture Key Laboratory of horticultural crop germplasm resources utilization, Institute of Fruit Tree Research, Chinese Academy of Agricultural Sciences (Xingcheng, Liaoning, China) and College of Horticulture Sciences, Shandong Agricultural University (Tai’an, Shandong, China). To ensure the consistency of the material, fruits were collected from the top of the inflorescence (first to mature). Samples were taken from plants under the same growth conditions for organ (root, stem, leaf, flower, and fruit)-specific expression. All samples were rapidly frozen in liquid nitrogen and stored at −80°C.