Table 1. Survey of existing plant genome-scale metabolic network reconstructions and some of their properties.
Rice, Oryza sativa; sorghum, Sorghum bicolor; sugarcane, Saccharum officinarum; tomato, Solanum lycopersicum.
| Model Organism | Context | No. of Compartments/Reactions/Metabolites | References |
|---|---|---|---|
| C3 plants | |||
| Arabidopsis | Heterotrophic cell culture | 2/1,336/1,231 | Poolman et al. (2009) |
| Arabidopsis (AraGEM) | Photosynthetic and nonphotosynthetic tissues | 5/1,567/1,748 | de Oliveira Dal’Molin et al. (2010) |
| Arabidopsis (iRS1597) | Photosynthetic and nonphotosynthetic tissues | 5/1,985/1,825 | Saha et al. (2011) |
| Arabidopsis (context and tissue specific) | Condition-specific models for compartmented cell, cell culture, cotyledon, flower bud, open flower, root, juvenile leaf, and silique | 7/1,929/1,410 | Mintz-Oron et al. (2012) |
| Arabidopsis | Heterotrophic cell culture | 5/2,769/2,618 | Cheung et al. (2013) |
| Arabidopsis | Leaf metabolism over a day-night cycle | 5/5,609/5,235 | Cheung et al. (2014) |
| Arabidopsis (AraCORE) | Photoautotrophically growing leaf cell | 4/549/407 | Arnold and Nikoloski (2014) |
| Arabidopsis | Plant primary and secondary metabolism | 8/6,399/6,236 | Seaver et al. (2015) |
| Arabidopsis | Multitissue whole-plant model | 6/9,727/10,733 | Gomes de Oliveira Dal’Molin et al. (2015) |
| Arabidopsis | Mesophyll and guard cell | 4/455/374 | Robaina-Estévez et al. (2017) |
| Arabidopsis | Root, stele, endodermis, cortex and epidermis (atrichoblasts), xylem, phloem, and pericycle cells | 8/2,199/1,813 | Scheunemann et al. (2018) |
| Rice | Developing leaf cell | 3/1,736/1,484 | Poolman et al. (2013) |
| Rice (iOS2164) | Single leaf cell | 7/2,441/1,999 | Lakshmanan et al. (2015) |
| Tomato (iHY3410) | Single leaf cell | 5/2,143/1,998 | Yuan et al. (2016) |
| C4 plants | |||
| Maize, sorghum, sugarcane (C4GEM) | Mesophyll and bundle sheath cells | 5/1,588/1,775 | Dal’Molin et al. (2010) |
| Maize (iRS1563) | Single cell | 5/1,798/1,820 | Saha et al. (2011) |
| Maize (iEB5204) | Single leaf cell | 12/1,535/1,125 | Bogart and Myers (2016) |
| Maize (iEB2140) | Single leaf cell | 12/635/603 | Bogart and Myers (2016) |
| Maize (iEB2140x2) | Mesophyll and bundle sheath cells in developing maize leaf | 19/1,268/1,121 | Bogart and Myers (2016) |
| Maize | Bundle sheath and mesophyll cells | 7/8,525/9,153 | Simons et al. (2014) |
| Maize (full and tissue specific) | Plant primary and secondary metabolism, leaf cell, embryo cell, endosperm cell | 8/6,458/6,250 | Seaver et al. (2015) |
| Crassulacean acid metabolism plants | |||
| Crassulacean acid metabolism | Leaf cell day-night cycle | 25/1,312/1,112 | Shameer et al. (2018) |