Allium

Root meristematic cells were obtained from seedlings: Allium cepa (2n = 2 × =16; chromosome size), A. fistulosum (2n = 2 × =16), A. schoenoprasum (2n = 2 × =16), A. altaicum (2n = 2 × =16), Linum usitatissimum (2n = 2 × =16), Triticum aestivum (2n = 6 × =42), Cannabis sativa (2n = 2 × =20).
Root meristematic cells were obtained from intensively grown plants in greenhouse: Allium roylei (2n = 2 × =16), A. wakegi (2n = 2 × =16), Humulus japonicus (2n = 2 × =17 for male or 2n = 2 × =16 for female plants), H. lupulus (2n = 2 × =20), Rosa wichurana (2n = 2 × =14), Populus nigra (2n = 2 × =38), Brassica oleracea (2n = 4 × =36), Ricinus communis (2n = 2 × =20), Anthurium andreanum (2n = 2 × =30), Monstera deliciosa (2n = 4 × =60), Philodendron scandens (2n = 2 × =32), Spathiphyllum wallisii (2n = 2 × =30), Syngonium auritum (2n = 2 × =24), Zantedeschia elliotiana (2n = 2 × =32), Aloe vera (2n = 2 × =14), Hippophae rhamnoides (2n = 2 × =24), Festuca arundinacea (2n = 6 × =42) and Lolium perenne (2n = 2 × =14), Thinopyrum ponticum (2n = 10 × =70), Th. elongatum (2n = 2 × =14).
Shoot meristems collected from seedlings for Triticum aestivum and Triticale (2n = 6 × =42) or from plants in the greenhouse for R. wichurana were also used as a source of divided cells for chromosome preparation.

Before assembly, we got high-quality reads by removing adaptor sequences and filtered low-quality reads by using TRIMMOMATIC^{54 (link)} from raw reads with parameters: ILLUMINACLIP:path/adaptor:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36. The resulting high-quality reads were de novo assembled and annotated with the TRINITY program^{55 (link)}. The commands and parameters used for running TRINITY were as follows: Trinity –seqType fq –JM 200G –left sample_1.fq –right sample_2.fq –normalize_by_read_set –CPU 32 –output sample –min_kmer_cov 2. Protein sequences and coding sequences of transcripts were predicted using TransDecoder (http://transdecoder.github.io), a software tool that identifies likely coding sequences from transcript sequences and compares the translated coding sequences with the PFAM domain database^{55 (link)}. For genes with more than one transcript, the longest one was used to calculate transcript abundance and coverage. Transcript abundance level was normalized using the fragments per kilobase per million mapped reads (FPKM) method, and FPKM values were computed as proposed by Mortazavi et al.^{56 (link)}.
Transcriptomes of Agave deserti^{57 (link)} and Allium cepa^{58 (link)} were downloaded from Dryad (h5t68) and NCBI (PRJNA175446), respectively. We removed the redundant unigenes in A. cepa by CD-HIT-EST with 99% identity and used TransDecoder to predict proteins with default parameters.
We carried out BLASTP (E value <1 × 10⁻³) to search the best hits for the proteins predicted in the transcriptomes against a customized database, built with proteins from the genomes of A. shenzhenica, P. equestris^{9 (link)}, D. catenatum^{10 (link)}, and A. officinalis (GenBank accession number GCF_001876935.1) as well as public databases, such as NCBI Plant RefSeq (release 80), Ensembl (release 77), Ensembl Metazoa (release 24), Ensembl Fungi (release 24), and Ensembl Protists (release 24). Only plant-homologous proteins were retained in the transcriptomes to eliminate the effects of genes derived from commensal organisms, laboratory contaminants, and artefacts resulting from incorrect assembly (Supplementary Table 13).

A roster of all persons aged 30–80 years was obtained from the offices of the Public Security Bureau, Bureau of Statistics, and Community Committee. Three-to-seven days before the baseline survey, the study staff distributed advertisement material to every household of the target community. A trained interviewer then completed a face-to-face interview. Interviewers were natives who knew the dialect of Taizhou to ensure smooth communication with the participants. After obtaining written informed consent, an in-person interview was conducted using a semi-structural questionnaire to collect baseline data. The interviewer-administered questionnaire covered socioeconomic status, demographic characteristics, residential history, personal habits (e.g., cigarette smoking, alcohol consumption, drinking of tea and coffee), dietary habits (semi-quantitative food frequency questionnaire), family history of selected diseases, cognitive function, physical activity (over the past 5 years and during adolescence), medical history, and, for women only, menstrual/reproductive history and use of hormone therapy. Lifetime occupational history was also obtained in the survey, including all jobs held for at least one year. For each job, the following information was obtained: name of workplace, job title, major products produced or handled, and the period over which each job started and ended. For dietary habits, the questionnaire was designed to capture information on consumption of major food items such as soy foods, allium-type vegetables, and cruciferous and dark-green, leafy vegetables (Table 1). The mean duration of the in-person interview took about 50 minutes.
After the interview, weight, height, waist and hip circumferences, and systolic and diastolic blood pressures were measured. Blood pressure was measured twice by a standardized mercury sphygmomanometer. Systolic blood pressure was recorded to the nearest 2 mmHg at the appearance of the first Korotkoff sound, and diastolic blood pressure was recorded to the nearest 2 mm Hg at the disappearance of the fifth Korotkoff sound. The first reading from each interviewer was discarded, and the second readings from two physicians were recorded and averaged. Weight and height were measured with subjects wearing only light indoor clothing and not wearing shoes. Waist circumference was measured midway between the caudal point of the costal arch as palpated laterally and the iliac crest. Hip circumference was measured at the symphysis-trochanter femoris level. Two measurements were taken, with a tolerance for differences of <1 cm for height, 0.5 cm for circumferences, and 1 kg for weight. A third measurement was taken if the difference between the first two measurements was larger than the defined tolerances.

The study area was located at the Linze Inland River Basin Integrated Research Station (LIRBIRS, 39° 21’ N, 100° 07’ E, 1,367 m above sea level) of the Ecosystem Research Network of the Chinese Academy of Sciences, in Pingchuan Town, Linze County, in the central part of the Hexi Corridor, Gansu Province, China (Figure 1A). The study area has a temperate continental desert climate, characterized by sparse precipitation throughout the year, which is concentrated in summer, as well as a dry climate, long day lengths, and intense solar radiation; the annual precipitation is 124.3 mm and the average annual temperature is 7.6°C. The annual average wind speed is 3.2 m·s^-1, the maximum wind speed is 21 m·s^-1, and the prevailing wind direction is northwesterly (Zhao et al., 2003 (link)). The precipitation and maximum wind speed dynamics during the fencing period (Figure 1C), which were determined using meteorological data obtained from the desert ecosystem meteorological long-term experiment sample sites at LIRBIRS, indicated fluctuations but no significant annual increases or decreases. The study area is dominated by semi-fixed dunes with a simple plant community structure and few species. Xerophytes and semi-shrubby vegetation dominate. The xerophytes and ultra-xerophytes do not typically include short-lived or annual plants. Representative plants include Reaumuria songorica, Nitraria tangutorum, Calligonum chinense, Haloxylon ammodendron, and Agriophyllum squarrosum, which exhibit a mixed spatial distribution, constituting a unique patch vegetation pattern. The dominant herb species are Artemisia scoparia, Suaeda glauca, Halogeton arachnoideus, and Eragrostis minor, with sporadic Zygophyllum kansuense and Allium mongolicum.

Homemade produced herby cheese samples subjected to metagenome analysis were collected from the provincial borders of Şırnak, Turkey (Table 1). The local manufacturing process of the herby cheese as follows; unpasteurized sheep milk was immediately fermented for 1 h using a starter culture. The specified plant leaves given in Table 1 were mixed with cheese samples. Then, the mixture was placed in cheesecloth and a weight was placed on it to drain the juice off for a day. On the next day, cheese was sliced and moved to saltwater for a week to solidify. Later on, the cheese was placed firmly in a plastic jar closing the lid tightly. For ripening, the cheese in the jar was buried into the soil for up to six months. Cheese samples were collected from 36 different localities of Şırnak province (Table 1). Here, we also analyzed non-herby cheese samples such as Sample 1 which was ripened in sheepskin, Sample 3, a curd cheese, and other two cheese samples which were manufactured as herby cheese without mixing any plant, Sample 5 and Sample 16 (Table 1). The collected cheese samples were transported to the sequencing laboratory in a foam box filled with dry ice in sterile tubes. Samples were stored in a freezer at −20 °C until analysis.Table 1

Localization of the cheese samples and herbs used to make herby cheese.

Table 1

Cheese Samples	Addition of herbs (Yes/No)	Localization	Herbs involved in cheese production
			Scientific name	Local name of herbs
1	No	İdil	Cheese ripened in sheepskin	–
2	Yes		Allium vineale L.	Sirik
3	No		Curd cheese	–
4	Yes		Heracleum persicum Desf.	So
5	No		Herb-free cheese	–
6	Yes	Beytüşşebab	Allium vineale L.	Sirik
7	Yes		Diplotaenia turcica Pimenov & Kljuykov	Siyabu
8	Yes		Allium vineale L.	Sirik
9	Yes		Diplotaenia turcica Pimenov & Kljuykov, Chaerophyllum macrospermum (Sprengel) Fisch. & C.A.Mey.	Siyabu-Mende
10	Yes		Diplotaenia turcica Pimenov & Kljuykov	Siyabu
11	Yes		Ferulago stellata Boiss	Bük
12	Yes	Uludere-1	Ferulago stellata Boiss	Bük
13	Yes		Allium vineale L., Allium cepa L.	Sirik-Pivaz
14	Yes		Ferulago stellata Boiss	Bük
15	Yes		Allium vineale L.	Sirik
16	No		Herb-free cheese	–
17	Yes	Uludere-2	Ferulago stellata Boiss	Bük
18	Yes		Allium vineale L., Gundelia tournefortii L. var. tournefortii L. Gundelia colemerikensis Fırat.	Sirik- Gerenk
19	Yes		Allium cepa L., Ferulago stellata Boiss	Pivaz-Bük
20	Yes		Allium cepa L.	Pivaz
21	Yes		Allium vineale L.	Sirik
22	Yes		Allium cepa L.	Pivaz
23	Yes		Allium cepa L.	Pivaz
24	Yes		Allium cepa L., Chaerophyllum macrospermum (Sprengel) Fisch. & C.A.Mey.	Pivaz-Mende
25	Yes		Ferulago stellata Boiss	Bük
26	Yes		Ferulago stellata Boiss	Bük
27	Yes		Allium cepa L., Chaerophyllum macrospermum (Sprengel) Fisch. & C.A.Mey.	Pivaz-Mende
28	Yes	Şenoba	Allium vineale L., Diplotaenia turcica Pimenov & Kljuykov	Sirik-Siyabu
29	Yes		Chaerophyllum macrospermum (Sprengel) Fisch. & C.A.Mey., Gundelia tournefortii L. var. tournefortii L. Gundelia colemerikensis Fırat.	Mende-Gerenk
30	Yes		Allium vineale L., Gundelia tournefortii L. var. tournefortii L. Gundelia colemerikensis Fırat.	Sirik- Gerenk
31	Yes	Beytüşşebab	Allium vineale L.	Sirik
32	Yes		Diplotaenia turcica Pimenov & Kljuykov	Siyabu
33	Yes	Cizre	Allium vineale L.	Sirik
34	Yes	İdil	Allium scorodoprasum L. subsp. rotundum (L.) Stearn	Kurat
35	Yes	Şırnak (Center)	Allium vineale L.	Sirik
36	Yes	Beytüşşebab	Ferulago stellata Boiss	Bük

This study was performed at the Ecological Restoration Experimental Site of Duolun County (1324 m a.s.l., 42°02′N, 116°17′E), a typical temperate steppe of the southern margin of the Mongolia Plateau. The mean annual air temperature and precipitation were 2.4°C and 382.2 mm, respectively. At this site, 90% of the annual precipitation falls between April and September. The potential evaporation, estimated by the Penman-Monteith equation using the original data acquired from Duolun meteorological station, ranged from 620 mm to 1416 mm (Li and Zhou, 2016 (link)). The potential evaporation greatly exceeds precipitation, indicating the study site is water-limited area. The hottest and coldest months are July (mean monthly temperature is 19.1°C) and January (mean monthly temperature is -17.3°C), respectively. Six perennial species including Stipa krylovii, Agropyron cristatum, Potentilla acaulis, Cleistogenes squarrosa, Allium bidentatum, and Artemisia frigida comprise of more than 70% of aboveground biomass. The soil is classified as a Haplic Calcisol according to the FAO classification, with sand, silt, and clay comprising 62.75%, 20.30%, and 16.95%, respectively. The soil aggregate and capillary porosities are 57.16% and 31.10%, respectively, at the depth of 0-10 cm (Su et al., 2021 (link)). The average rooting depth is 11.6 cm.