Table 1.
Structural characteristics and physio-chemical properties of dicer-like (DCL), argonaute (AGO) and RNA dependent RNA polymerase (RDR) genes from S. spontaneum.
| Gene name | Gene ID | Location | Protein | |||||
|---|---|---|---|---|---|---|---|---|
| Chromosome | Start | End | CDS (bp) | Length (aa) | Mw (Da) | PI | ||
| Dicer-like (DCL) | ||||||||
| SsDCL1a | Sspon.01G0001230-3D | Chr1D | 3,692,925 | 3,701,074 | 4,377 | 1,458 | 163,204.71 | 6.05 |
| SsDCL1b | Sspon.01G0001230-1A | Chr1A | 3,976,165 | 3,983,525 | 4,770 | 1,590 | 178,065.62 | 6.05 |
| SsDCL2 | Sspon.01G0022370-1A | Chr1A | 81,960,057 | 81,976,273 | 3,699 | 1,233 | 139,512.97 | 7.06 |
| SsDCL3 | Sspon.01G0019860-4D | Chr1D | 71,661,374 | 71,672,007 | 4,752 | 1584 | 179,009.05 | 6.24 |
| Argonaute (AGO) | ||||||||
| SsAGO2a | Sspon.05G0030950-2D | Chr5D | 11,880,179 | 11,884,678 | 3,066 | 1,021 | 111,963.65 | 8.73 |
| SsAGO2b | Sspon.05G0037340-1D | Chr5D | 11,924,233 | 11,928,734 | 2,763 | 921 | 100,646.66 | 7.81 |
| SsAGO3a | Sspon.05G0030960-1C | Chr5C | 2,396,093 | 2,401,132 | 3,048 | 1,015 | 110,049.24 | 9.30 |
| SsAGO3b | Sspon.05G0030950-1C | Chr5C | 2,386,282 | 2,391,173 | 2,904 | 967 | 104,620.95 | 9.27 |
| SsAGO3c | Sspon.05G0030950-1P | Chr5D | 12,513,102 | 12,517,597 | 3,036 | 1,011 | 109,860.1 | 9.35 |
| SsAGO4 | Sspon.02G0016200-2D | Chr3D | 39,536,146 | 39,547,268 | 2,838 | 946 | 105,523.71 | 8.60 |
| SsAGO5a | Sspon.01G0028360-2B | Chr1B | 96,848,274 | 96,854,895 | 3,165 | 1,054 | 115,793.38 | 9.42 |
| SsAGO5b | Sspon.01G0014460-3D | Chr1D | 87,130,069 | 87,135,808 | 2,742 | 913 | 102,643.41 | 9.28 |
| SsAGO5c | Sspon.01G0014460-1A | Chr1A | 41,213,733 | 41,219,461 | 2,418 | 806 | 90,379.42 | 9.55 |
| SsAGO5d | Sspon.01G0014460-2B | Chr1B | 96,914,953 | 96,920,845 | 2,784 | 927 | 103,595.76 | 9.55 |
| SsAGO6a | Sspon.07G0020900-1A | Chr7A | 78,332,899 | 78,336,592 | 1,902 | 634 | 70,983.26 | 9.46 |
| SsAGO6b | Sspon.07G0020900-2D | Chr7D | 60,984,388 | 60,994,488 | 2,070 | 689 | 77,218.74 | 9.34 |
| SsAGO10a | Sspon.08G0006580-1P | Chr8D | 17,872,226 | 17,876,344 | 2,271 | 757 | 83,975.06 | 9.22 |
| SsAGO10b | Sspon.08G0006580-1A | Chr8A | 20,403,262 | 20,409,634 | 2,829 | 942 | 105,347.29 | 9.47 |
| SsAGO10c | Sspon.08G0006580-2B | Chr8B | 18,085,409 | 18,091,645 | 2,394 | 797 | 88,300.59 | 9.67 |
| SsAGO10d | Sspon.08G0006580-4D | Chr8D | 17,765,548 | 17,771,337 | 1,884 | 628 | 71,264.01 | 9.40 |
| SsAGO10e | Sspon.08G0006580-3C | Chr8C | 9,379,029 | 9,385,180 | 2,916 | 971 | 108,586.36 | 9.43 |
| SsAGO18a | Sspon.02G0007830-1A | Chr2A | 22,748,211 | 22,753,686 | 3,099 | 1,032 | 113,076.36 | 9.47 |
| SsAGO18b | Sspon.01G0024300-1A | Chr1A | 87,229,183 | 87,234,462 | 2,382 | 793 | 88,734.95 | 9.29 |
| SsAGO18c | Sspon.01G0024300-3D | Chr1D | 84,919,502 | 84,924,770 | 2,364 | 787 | 88,118.01 | 9.00 |
| SsAGO18d | Sspon.02G0007830-2D | Chr2D | 16,391,380 | 16,396,270 | 2,754 | 918 | 100,666.07 | 9.44 |
| RNA dependent RNA Polymerase (RDR) | ||||||||
| SsRDR1a | Sspon.04G0003980-2D | Chr4D | 12,916,500 | 12,921,015 | 3,324 | 1,107 | 126,692.84 | 7.73 |
| SsRDR1b | Sspon.04G0003980-1A | Chr4A | 12,309,373 | 12,314,472 | 3,348 | 1,115 | 127,601.91 | 7.53 |
| SsRDR2a | Sspon.05G0009620-1A | Chr5A | 27,714,217 | 27,719,638 | 3,414 | 1,137 | 126,512.75 | 6.67 |
| SsRDR2b | Sspon.05G0009620-2B | Chr5B | 22,682,674 | 22,688,038 | 3,315 | 1,104 | 122,789.35 | 6.50 |
| SsRDR2c | Sspon.05G0009620-3C | Chr5C | 19,106,947 | 19,112,258 | 3,414 | 1,137 | 126,557.88 | 6.39 |
| SsRDR2d | Sspon.05G0009620-4D | Chr5D | 30,160,562 | 30,165,865 | 2,967 | 989 | 110,364.29 | 7.29 |
| SsRDR3 | Sspon.05G0014430-3C | Chr5C | 48,023,413 | 48,044,408 | 2076 | 691 | 79,290.78 | 7.29 |
| SsRDR4 | Sspon.05G0014430-4D | Chr5D | 52,146,251 | 52,168,613 | 2049 | 683 | 77,901.79 | 6.25 |
| SsRDR5 | Sspon.03G0023160-2C | Chr3C | 89,299,759 | 89,307,281 | 2,514 | 838 | 96,153.93 | 8.70 |
| SsRDR6a | Sspon.08G0019290-1B | Chr8B | 11,200,927 | 11,205,278 | 3,240 | 1,079 | 120,677.59 | 7.10 |
| SsRDR6b | Sspon.08G0019290-2D | Chr8D | 11,219,834 | 11,222,839 | 3,006 | 1,001 | 111,860.59 | 8.24 |
CDS coding sequence, MW molecular weight, IP isoelectric point.