SorghumBase, a web portal for comparative plant genomics focused on sorghum crop varieties, has now released its second version. The release provides access to 13 new sorghum varieties (Tao et al, 2021), for a total of 18 sorghum reference genomes, and 6 other species to support phylogenetic analyses, and cross-species comparisons. The genome databases were built in direct collaboration with the Gramene and Ensembl Plants projects. Other data sets were facilitated via collaborations with the Expression Atlas, the Sorghum QTL Atlas, and the Plant Reactome databases. Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 59-8062-9-002).
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13 new sorghum reference genomes:
- Sorghum bicolor ssp. bicolor IS12661
- Sorghum bicolor ssp. bicolor IS3614-3
- Sorghum bicolor ssp. bicolor IS38525
- Sorghum bicolor ssp. bicolor IS929
- Sorghum bicolor ssp. bicolor Ji2731
- Sorghum bicolor ssp. bicolor R931945-2-2
- Sorghum bicolor ssp. bicolor (margaritiferum) IS19953
- Sorghum bicolor ssp. bicolor (margaritiferum) PI525695
- Sorghum bicolor ssp. drummondii PI532566
- Sorghum bicolor ssp. verticilliflorum AusTRCF317961
- Sorghum bicolor ssp. verticilliflorum 353
- Sorghum bicolor ssp. verticilliflorum PI536008
- Sorghum propinquum S369-1
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The new Sorghum genomes (see above), together with the original five Sorghum bicolor bicolor genomes (BTx623, Rio, Tx2783, Tx430, and Tx436), and 6 plant outgroup species (Japonica rice, B73 maize (assembly versions 4 and 5), Arabidopsis thaliana, grapevine, a vascular plant, and a single-celled green algae), were used to build 30,475 protein-coding gene family trees. The database also includes a total of five pairwise DNA alignments for each of the sorghum genomes aligned to Japonica rice.
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We continue to host genetic, structural and phenotypic variation, gene expression and orthology-based pathway projections for the reference genome S. bicolor BTx623.
Gene Trees. A total of 30,475 protein-coding gene family trees were constructed using the peptide encoded by the canonical transcript (i.e., a representative transcript for a given gene) for each of 796,813 individual genes (836,223 input proteins) from 25 plant genomes.
Whole-Genome Alignments. There are pairwise genomic alignments for each one of the following sorghum genomes against Japonica rice:
- Sorghum bicolor ssp. bicolor BTx623
- Sorghum bicolor ssp. bicolor RTx430
- Sorghum bicolor ssp. bicolor RTx436
- Sorghum bicolor ssp. bicolor Tx2783
- Sorghum bicolor ssp. bicolor Rio
Genetic variation data sets for over 6.7 million sorghum single nucleotide polymorphisms (SNPs) (Morris et al, 2013; Mace et al, 2013) and 1.5 million chemically induced by ethyl methanesulfonate (EMS) point mutations (Xin et al, 2008); 27,884 structural variants (Zheng et al, 2011) from the Database of Genomic Variation Archive (DGVa); and nearly 6,000 QTLs from the Sorghum QTL Atlas.
Gene expression data for the S. bicolor BTx623 genome reference was curated and processed through the EMBL-EBI Expression Atlas. The set consists of seven studies with baseline expression in BTx623 (Davidson et al, 2012; Makita et al, 2014; Wang et al, 2018; Emms et al, 2016; Turco et al, 2017; and two unpublished studies with SRA projects SRP062564 and SRP029353). At the Expression Atlas site, baseline expression is also available for a bioenergy sorghum genotype R.07020 (Kebrom et al, 2017), and differential expression for three studies (Varoquaux et al, 2019; Dugas et al 2011; Gelli et al, 2014), including one (Dugas et al, 2011) in the BTx623 reference.
For the baseline studies in SorghumBase, sampling was done in a single site (e.g., stem internode), a discrete cell type (e.g., bundle sheath, leaf mesophyll), organism parts (including seed, spikelet, stem, leaf, flag leaf, inflorescence, pistil, embryo, endosperm, anther, pericarp, pollen, root, shoot, floral meristem, flower, vegetative meristem, vascular/ non-vascular system) or the whole organism, at one or multiple developmental stages. For example, Wang and collaborators (Wang et al, 2018) examined 11 matched tissues of maize B73 and sorghum BTx623 at different developmental stages for gene expression profiling totalling 165 experimental assays.
269 orthology-based sorghum pathways associated with 1,248 S. bicolor BTx623 genes. These were projected from curated Japonica rice pathways and are linked to Gramene’s Plant Reactome.
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