SetariaDB-Manual

I - SEARCH

II - MULTI-OMICS

2.1 - Variome

2.2 - Phenotype

III - TOOLS

IV - RESOURCE DOWNLOAD

Setaria-db focuses on integrating reference genomes, genomic variations, germplasms, and multi-omics data of foxtail millet into a database, and establishing their relations to assist the foxtail millet community for better genetic resources exploration and breeding.

I - SEARCH

Located on the homepage, this is a gateway linking to all gene- or annotations- related function throughout the entire database.

II - MULTI-OMICS

This module allows users to search for genomic, transcriptomic, and metabolomic variations across diverse natural accessions currently accessed.

2.1 Variome

Both Yugu1 T2T-based and Yugu1 v2.2-based genomic variants (including SNPs, InDels, and SVs) are provided for the 113 assembled genomes and 1,844 global germplasms. Users can peruse variation details for any desired accession or region.

Data Sources	Reference	Yugu1_v2.2
	Reference	Yugu1_T2T
	Data Set	1844 world-wide germplasms
	Data Set	112 pan-genome
Variation Search	CHROM	Chr1~Chr9
	TYPE	ALL/INDEL/SNP/SV
	POS	Physical locations can also be input to show the variations in the segment.
	GENE ID	Input foxtail millet gene ID, Ex: Seita.7G390300
	SAMPLES	Input a foxtail millet sample name or sample set, Ex: WGS0202

2.2 Phenotype

In this module, 226 phenotype datasets, which including 60 traits from 13 distinct geographic loci across 11 years are provided. Users can check and download all datasets apply for genome wide association studies or genomic predication or haplotype analysis with genomic variants data.

Geographic Distribution	The geographic location where the trait was collected is shown on a map of China, with the number representing the number of samples where the trait was collected at that geographic location.
Trait Distribution	Distribution of all samples across all years and geographic locations.
Location Distribution	Demonstrate distribution of traits by different environments
Year Distribution	Demonstrate the distribution of traits in different years.

2.3 Transcriptome

Transcriptome modules provide the search function for gene expression of Yugu1, Ci846, and A10 across approximately 28 tissue types and various growth stages, along with the grain transcriptome of 312 foxtail millet germplasms during the late grain filling stage.

2.3.1 Multiple-Tissues

In multiple-Tissues, users can input a single target gene and select a germplasm (wild: A10, landrace: Ci846 and elite line: Yugu1) to check the expression pattern of the gene in different tissues at different stages.

2.3.2 Multiple-Samples

In multiple-Samples, the gene expression could be check and display with heatmap for different germplasms.

2.4 Metabolome

2.5 Correlations

This module designed for in-depth data study, it will facilitate correlation analyses between phenotype-vs-transcriptome, phenotype-vs-metabolome, and transcriptome-vs-metabolome.

III - TOOLS

In this module we provide toolkits such as BLAST, JBrowse, Primer, CRISPR design, GO & KEGG enrichment analysis, and Correlation analysis.

3.1 BLAST

3.2 JBrowse

Genome browser is launched by JBrowse2. The Yugu1_T2T is provided as reference genome. The gene annotation, ATAC-seq, ChIP-seq, HiC,RNAseq and SV variation are also can be viewed.

3.3 Primer Design

3.3.1 Design primers by reference position

3.3.2 Design primers with input sequence

3.4 GO & KEGG

3.5 Correlations

In the correlation analysis module, there are three functions that can be selected and executed: Phenotype -vs - Transcription, Phenotypic -vs- Metabolic and Metabolism -vs- Transcription.