Additional file 2: Figure S1. of An approach of identifying differential nucleosome regions in multiple samples

Nucleosome occupancy profiles in the vicinity of transcription start sites (TSSs) for 5419 genes in 22 mutant strains. Figure S2. A sample of identification of differential nucleosome regions (DNRs) with local and global background correction methods, respectively. Figure S3. A, Shown are reads count profiles which are normalized with the windows with a different width. B, Shown is average of coefficient of variation (CV) in each window against the width of window in the four mutant strains. The result suggests the background correction with a small window (<200 bp) will eliminate variation of nucleosome. Figure S4. An enrichment analysis for the nucleosome-dynamic genes. A gene with a differential nucleosome region is regarded as a nucleosome-dynamic gene. (PDF 346 kb

Data_Sheet_1_Response of rhizosphere microbial community of Chinese chives under different fertilization treatments.docx

Soil microorganisms play an irreplaceable role in agricultural production, however, an understanding of response of soil microorganisms to slow-release and common fertilizer applications is limited. In this study, different amounts of slow- release fertilizer were used to overwintering Chinese chives growing area in a plastic greenhouse to investigate the effects of on rhizosphere soil physicochemical properties and soil microbial communities (bacteria and fungi) of Chinese chives. The result displayed that application of slow-release fertilizer significantly improved soil nutrients, soil enzyme activity, and soil microbial community structure and diversity compared to conventional fertilizer application. Compared with T1 treatment, the content of total nitrogen (TN) and available phosphorus (AP), and the SU-E activity in the soil of T2 (NPK: 62.8 kg · 667 m-2) increased by 42.58%, 16.67%, and 9.70%, respectively, showing the best effects. In addition, soil bacterial diversity index and soil microbial community structure were improved as indicated by increased relative abundance of each species, such as Byssovorax, Sandaracinus, and Cellvibrio. Oppositely, the both soil fungal diversity and the number of species decreased after fertilizationthe relative abundance of Ascomycota increased in each fertilization treatment detected by ITS sequencing. Further, the relative abundance of pathogenic fungi such as Pezizomycetes, Cantharellales, and Pleosporales decreased in the T2 treatment. Principal Coordinates Analysis (PCoA) showed that both the amount of fertilizer applied and the type of fertilizer applied affected the soil microbial community structure. RDA evidenced that soil bacteria, Proteobacteria and Gemmatimonadetes, were closely correlated with soil AN, SOM, and AK. Acidobacteria were closely correlated with soil pH, TN, and AP. Ascomycota was closely correlated with soil pH and TN. In conclusion, the application of slow-release fertilizers and reduced fertilizer applicationcould improve soil physical and chemical properties as well as soil microbial community structure and diversity, contributing to sustainable soil development. The recommended fertilization rate for overwintering Chinese chives is NPK: 62.8 kg · 667 m−2.</p

Schematic representations for chromosomal distribution and interchromosomal relationships of lettuce <i>ZIP</i> genes.

Different colored lines indicate all synteny blocks in the lettuce genome. The red line indicates a gene pair that is duplicated with LsZIP genes. The chromosome number is indicated at the top of each chromosome. The black text indicates the gene name of the LsZIP family, and the gray text indicates the gene name that has a collinearity relationship with the LsZIP genes. The lengths of the chromosomes are marked using scales, with each small scale indicating 500,000 amino acids, and every 25th scale is marked using a number.</p

The sequences of primers used for qRT-PCR.

(DOCX)</p

Phylogenetic tree and gene structure analysis of ZIP gene family.

(A): phylogenetic analysis of 133 ZIP genes from 15 plant species. The phylogenetic tree was constructed using the NJ method. The blue and red rect on the tree indicate Monocot (8) and Dicots (7) species, respectively. The phylogeny tree was visualized by EvolView (https://evolgenius.info//evolview-v2). (B): phylogenetic relationships, gene structure, and architecture of conserved protein motifs in ZIP genes from lettuce and the LsZIP proteins annotated with the MEME server. (B-a): phylogenetic tree was constructed based on the full-length sequences of lettuce ZIP proteins using MEGA 7 Software. Details of clusters are shown in different colors. (B-b): Exon-intron structure of lettuce ZIP genes. Yellow boxes indicate exons; black lines indicate introns. (B-c): motif composition of lettuce ZIP proteins. Motifs, numbered 1–12 are shown in different colored boxes; the corresponding sequence is shown in B-d.</p

Predicted secondary structure of lettuce <i>ZIP</i> protein.

(DOCX)</p

Heatmap representation of the expression levels of 20 <i>LsZIP</i>s among different treaments.

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses were used to assess the transcript levels of LsZIPs in leaves sampled at 0 h, 12 h,24h and 48 h after different treatment in lettuce seedlings. Lower and higher levels of expression levels are indicated by red and blue, and the median level is indicated by white. The heatmap was constructed using TBtools. Where A: represents the relative expression of 20 LsZIP genes under Zn-excess treatment; B: represents the relative expression of 20 LsZIP genes under Zn-deficiency treatment; C: represents the relative expression of 20 LsZIP genes under Fe-excess treatment; D: represents the relative expression of 20 LsZIP genes under Fe-deficiency treatment; and E: Relative expression of 20 LsZIP genes in response to Cd stress.</p

List of <i>ZIP</i> genes in lettuce.

Note: a: Name of gene model was modified from the annotation of the lettuce genome v7 (from NCBI), the prefix ‘Ls’ indicating the lettuce species abbreviated from L. sativa; b: NCBI database unique digital identifier for the gene; c: Lo-cations represent the coding region of the gene. can estimate of the stability of your protein in a test tube, a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable. (DOCX)</p

KA/KS of 20 <i>LsZIP</i> genes.

(DOCX)</p

Tertiary structure prediction of 20 <i>LsZIP</i> proteins.

Using the protein homology modeling method based on the LsZIP structure of the swiss-model database, the structure with the highest score was chosen as the optimal structure for the LsZIP protein.</p