Citable datasets (some associated with publications or preprints and some stand alone).
- Schnable JC, Zhang Y, Ngu DWC. (2016) Pan-Grass Syntenic Gene Set (sorghum referenced). figShare. 10.6084/m9.figshare.3113488.v1
Syntenic gene list for a bunch of species. Splits out maize1 and maize2 subgenomes. Uses maize v3, sorghum v3, setaria v2.2 and rice v7 (among others). Constructed using LastZ to identify homologous genes, QuotaAlign to identify syntenic regions and python polishing scripts to identify high confidence orthologs within syntenic blocks.
- Schnable JC, Lyons E. (2015) Plant Paleopolyploidy. figShare.
Best effort attempt to describe the positioning and evidence supporting different known whole genome events relative to the phylogeny of all plant genomes sequenced at the time. Also on CoGePedia.
- Schnable, JC (2015) Maize and Sorghum Genesets. figShare.
BED files answering the question: Where would each sorghum gene be in each maize subgenome if there were zero fractionation after the maize WGD? Also some useful figures generated using the same data.
- Schnable JC. (2015) Sequenced Plant Genomes. CoGePedia Wiki Page
Exhaustive list of published plant genomes as of early 2015.