sorghum3_intell_plusteff.csv (12.81 MB)

Grass Syntenic Gene List sorghum v3 maize v3/4 with teff and oropetium v2

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posted on 29.03.2019 by James Schnable
This pan-grass synteny list was generated using the methodology described in:

Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. (2017) “Differentially regulated orthologs in sorghum and the subgenomes of maize.” The Plant Cell doi: 10.1105/tpc.17.00354 bioRxiv preprint doi: 10.1101/120303

Here the species analyzed are sorghum (BTx623 version 3), maize (both B73_refgen3 and B73_refgen4, treated as separate species for the purpose of this analysis), Setaria viridis (v1), Setaria italica (Yugu1 v2.2), Oropetium (v1), Brachypodium distachyon, and rice (MSU v7).

Both maize v3 and maize v4 were split into subgenomes using the definitions first published in:

Schnable JC, Springer NM, Freeling M. (2011) “Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.” PNAS doi: 10.1073/pnas.1101368108

Note that this version includes a revised an much improved Oropetium genome published in Plant Direct: https://doi.org/10.1002/pld3.96 and a chromosome level teff genome currently posted as a preprint to BioRxiv: https://doi.org/10.1101/580720

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