About database content
SoyTIPdb is a soybean transposon element(TE) insertion polymorphism database which contains the reference TE insertion absences and non-reference TE insertion presences in 5,521 soybean accessions collected from previously published studies. The collected accessions come from more than 45 countries and 160 regions representing most comprehensive genetic diversity. In addition to the collected accessions, and the reference TE insertion absences and the non-reference TE insertion presences in the collected accessions, the reference genes, the reference TEs, reference TE insertions harbored in the reference genome Zh13_v2, together with the gene expression levels, are all integrated into the database.
Furthermore, selective analysis of TE insertion in global populations such wild, landrace and cultivar, as well as populations of different country origins were pre-calcualted and the analysis results are also gathered in the database for users to search or view.
Quick tutorial (click items to show/hide details)
Search germplasm accession
Through the search menu, users can search soybean germplasm accessions by bioproject, origin country and variety type.
Details of germplasm accession
The details of a soybean accessions including: 1) basic information; 2) geographical origin map; 3) TE family distribution of the detected reference TE insertion absences and non-reference TE insertion presences; 4) Gene element distribution of the detected reference TE insertion absences and non-reference TE insertion presences; 5) Chromosome position distribution of the detected reference TE insertion absences and non-reference TE insertion presences; 6) Tables of the detected reference TE insertion absences and non-reference TE insertion presences.
Search transposon elements
The the search menu, users can search transposon elements by genomic region, transposon family and associated genes.
Details of transposon element
The details of a transposon element include 3 sections: 1) basic information; 2) Jbrows showing it in the genomic context; 3) Heat map showing expression levels of nearest genes in tissues.
Search reference TE insertion polymorphisms
Through the search menu, users can open a page to search reference TE insertion polymorphisms by genomic region, TE family and associated genes.
Details of a reference TE insertion polymorphisms
The details of reference TE insertion include 6 sections: 1) Basic information; 2) JBrowse showing it in the genomic context; 3) Distribution of accession with the reference TE insertion absences; 4) Geographic location of accessions with the reference TE insertion absence; 5) Table of accession with the reference TE insertion absence; 6) Heat map showing expression levels of the nearest genes in tissues.
Search non-reference TE insertion polymorphisms
Through the search menu, users can open a page to search non-reference TE insertion polymorphisms. Non-reference TE insertion regions can be queried by genomic region, transposon element family and associated genes. Click on the detail icon to open a new page showing the details of non-reference TE insertion polymorphisms.
Details of a non-reference TE insertion polymorphisms
A non-reference TE insertion region includes 5 sections: 1) Basic information; 2) Distribution of accession in geographic location; 3) Geographic location distribution of accessions with non-reference TE insertion. 4)Table of accessions and insertion details. 5) Heat map showing expression levels of nearest genes.
Selective analysis of TE insertion between populations
Through the analysis menu, users can open a page to search and view selective analysis results of TE insertion between different populations.
Browse TEs and TE insertion polymorphisms
Through the JBrowse menu, users can open the pages to view reference TEs, reference TE insertions, reference TE insertion absences and non-reference TE insertion presences in JBrowse.
Download datasets
Through the download menu, users can open the download page to obtaion reference TE insertion absences and non-reference TE insertion presences in each soybean accession.
Contact
Jinding Liu
liujd@njau.edu.cn
References
The published papers providing proteomics data are as follows:
Liu et al. (2020). Pan-Genome of Wild and Cultivated Soybeans. Cell 182(1):162-176.e13. doi: 10.1016/j.cell.2020.05.023. Epub 2020 Jun 17.
Lu et al. (2020). Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nature Genetics 52(4):428-436. doi: 10.1038/s41588-020-0604-7. Epub 2020 Mar 30.
Kim et al. (2021). The patterns of deleterious mutations during the domestication of soybean. Nature Communications 12(1):97. doi: 10.1038/s41467-020-20337-3.
Bayer et al. (2022). Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. Plant Genome 15(1):e20109.doi: 10.1002/tpg2.20109. Epub 2021 Jun 24.
Liu et al. (2022). Putative variants, genetic diversity and population structure among Soybean cultivars bred at different ages in Huang-Huai-Hai region. Scientific Reports 12(1):2372. doi: 10.1038/s41598-022-06447-6.