Table 1.
Summary of all the transcriptome data
| Species | Type | Breed | Sample size | Tissue | Data sources |
|---|---|---|---|---|---|
| Rice | Dome | Oryza sativa indica | 9 | panicle | This study |
| Dome | Oryza sativa japonica | 11 | panicle | ||
| Wild | Oryza nivara | 10 | panicle | ||
| Wild | Oryza rufipogon | 10 | panicle | ||
| Soybean | Improved | Glycine max | 11 | stem apical meristems | This study |
| Landrace | Glycine max | 14 | stem apical meristems | ||
| Wild | Glycine soja | 10 | stem apical meristems | ||
| Maize ear | Dome | Maize | 12 | ear | [29] |
| Wild | Teosinte | 18 | ear | ||
| Maize leaf | Dome | Maize | 12 | leaf | |
| Wild | Teosinte | 17 | leaf | ||
| Maize stem | Dome | Maize | 12 | stem | |
| Wild | Teosinte | 17 | stem | ||
| Cotton | Dome | Gossypium hirsutum | 40 | leaf | [28] |
| Wild | 10 | leaf | |||
| Silkworm | Dome | Bombyx mori (trimolter) | 4 | silk gland | This study |
| Wild | Bombyx mandarina | 4 | silk gland | ||
| Dog | Dome | Dog | 5 | brain frontal cortexes | [22] |
| Wild | Grey wolf | 6 | brain frontal cortexes | ||
| Chicken | Dome | Avian broiler | 5 | gastrocnemius | [21] |
| Wild | Red junglefowl | 4 | gastrocnemius |
Dome represents the domestic species, while wild represents the wild progenitor species. Panicles of rice samples, stem apical meristems of soybeans and silk glands of silkworms were sequenced by us. The domestic silkworm samples were from four trimolter silkworm breeds (Additional file 1: Table S3). A few of the samples which had lower mapping depths were discarded in the following analysis (Additional file 2: Table S8)