Table 1.
Annotated Genes in Sugarcane BACs and Their Orthologous Relationships with Sorghum and Rice Genes
| Genomic Region | Gene No. | Functional Annotation | BLASTX E-Value | Orthologous Locus in Sorghum | Orthologous Locus in Rice |
|---|---|---|---|---|---|
| LFY | 1 | Brachypodium distachyon COBW domain-containing protein 1-like | 0.0E+00 | Sb06g027386 | Os04g51100 |
| 2 | Oryza sativa Indica Group hypothetical protein OsI_17248 | 0.0E+00 | Sb06g027382+ Sb06g027384c | Os04g51090 | |
| 3 | Zea mays scramblase family protein | 0.0E+00 | Sb06g027380 | Os04g51080 | |
| 4 | Zea mays WAK53a–OsWAK receptor-like protein kinase precursor–Pseudogene | 0.0E+00 | Sb01g013060 | Os04g51040 and Os04g51050d | |
| 5a | Zea mays wall-associated receptor kinase 1-like isoform X2–Pseudogene | – | – | – | |
| 6 | Brachypodium distachyon wall-associated receptor kinase-like 17-like | 0.0E+00 | Sb06g027350+ Sb06g027360c | Os04g51030 | |
| 7b | Brachypodium distachyon wall-associated receptor kinase-like 17-like | – | – | – | |
| 8b | Brachypodium distachyon wall-associated receptor kinase-like 17-like - Pseudogene | – | – | – | |
| 9 | Zea mays floricaula/leafy-like 2 | 5.0E−171 | Sb06g027340 | Os04g51000 | |
| 10 | Zea mays 60S ribosomal protein L12 | 1.0E−108 | Sb06g027330 | Os04g50990 | |
| 11 | Zea mays seed specific protein Bn15D1B | 6.0E54− | Sb06g027320 | Os04g50970 | |
| 12 | Sorghum bicolor hypothetical protein | 0.0E+00 | Sb06g027315 | Os04g50960 | |
| PHYC | 1 | Hordeum vulgare voltage-dependent outwardly rectifying plasma membrane K+ channel KCO1/TPK1 | 0.0E+00 | Sb01g007830 | Os03g54100 |
| 2 | Zea mays meiotic recombination protein SPO11 | 0.0E+00 | Sb01g007840 | Os03g54091 | |
| 3b | Hordeum vulgare voltage-dependent outwardly rectifying plasma membrane K+ channel KCO1/TPK1–Pseudogene | – | – | – | |
| 4 | Zea mays phytochrome C1 apoprotein | 0.0E+00 | Sb01g007850 | Os03g54084 | |
| 5 | Sorghum bicolor hypothetical protein | 3.0E−27 | Sb01g007870 | Os03g54050 | |
| 6 | Eulaliopsis binata embryonic flower 2 protein | 0.0E+00 | Sb01g007878 | Os09g13630 | |
| 7 | Zea mays glutathione transporter | 0.0E+00 | Sb01g007880 and Sb01g007900d | Os03g54000 | |
| 8 | Oryza sativa Japonica Group hypothetical protein | 0.0E+00 | Sb01g007890 and Sb01g007910+ Sb01g007920c, d | Os03g53990 | |
| 9 | Sorghum bicolor hypothetical protein | 8.0E−69 | Sb01g007930 | Os03g53980 | |
| TOR | 1 | Setaria italica predicted DNA primase small subunit-like–Pseudogene | – | – | – |
| 2 | Setaria italica predicted serine/threonine-protein kinase TOR-like | 0.00E+00 | Sb09g017790 | Os05g14550 |
a
The pseudogene does not have orthologous counterpart in sorghum and rice genomic region.
b
Duplicated gene.
c
Sorghum genes edited into one gene based on the structure of their orthologous counterparts in rice (Oryza sativa), maize (Zea mays), and Brachypodium (Brachypodium distachyon). These loci were named Sb06g027350 + Sb06g027360, Sb06g027382 + Sb06g027384, and Sb01g007910 + Sb01g007920.
d
The predicted gene in sugarcane has orthology with two distinct genes in the related species (fig. 1).