Table 1. Results for positive selection tests and characteristics for the 14 clusters.
| |
|
|
|
M0 vs M3 |
M7 vs M8 |
MEME |
||||
|---|---|---|---|---|---|---|---|---|---|---|
| Maize Gene | Genome Annotation | Cluster | Species | ω | Δ2L | ω | Δ2L | PSS (BEB) | PSS | |
| GRMZM2G149800 |
Hypothetical protein LOC100277913 |
31469106-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, Pe |
24.09 |
245.65 |
2.59 |
21.2360 |
None |
71T, 227R, 232S, 342Y |
|
| GRMZM2G324297 |
Unknown (similar to arogenate dehydrogenase) |
31456723-e |
Zm, Si, Bd, Os, Sb, Ta, Hv |
1.10 |
470.95 |
1.30 |
17.4570 |
151Q**, 158R, 240K, 253D, 257A, 306S, 323Q, 349R, 368F |
147A, 182S, 211L, 301S, 358R |
|
| GRMZM2G453805 |
Chitinase class III |
31466309-se |
Zm, Si, Bd, Os, Sb, Ta, Pe |
6.83 |
216.60 |
7.31 |
14.2870 |
4A**, 9A, 260P, 285I* |
87G, 138G, 160S, 169A, 184L, 222G, 224A, 269I, 282I, 293V |
|
| GRMZM2G168502 |
Hypothetical protein LOC100217285 |
31477240-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, Pe |
0.83 |
222.73 |
3.85 |
10.2076 |
130V, 347S*, 356T |
32V, 99N, 120N, 144A, 184V, 203C, 206A, 235E, 293S, 296C |
|
| GRMZM2G056369 |
Putative Isocitrate lyase |
31452004-e |
Zm, Si, Bd, Os, Sb, Ta, Hv |
0.40 |
145.16 |
1.10 |
8.5392 |
30G, 76G, 334K, 345R, 371T, 560P, 561R, 564T, 572M |
142L, 293S, 320C, 330G, 331V, 344D, 345R |
|
| GRMZM2G402631 |
Pathogenesis-related protein 5 |
31443992-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, As, Pe, Sc, Or, Tm |
1.12 |
201.12 |
1.31 |
8.3213 |
57P, 91Q, 148V, 166M |
39G, 53T, 56N, 58G, 84G, 98A, 109L, 146R, 182T, 185P |
|
| GRMZM2G465226 |
Pathogenesis-related protein 1 |
31458297-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, Pe |
0.79 |
219.62 |
7.57 |
1.8310 |
None |
99S, 108D, 128A, 134V |
|
| GRMZM2G338809 |
Hypothetical protein LOC100382111 |
31445034-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, Pe |
0.33 |
272.13 |
1.63 |
0.5130 |
None |
35T, 37A, 121F, 131A, 266V, 271S, 278C, 342I, 393K, 413A |
|
| GRMZM2G011085 |
Putative uncharacterized protein |
31447249-e |
Zm, Si, Bd, Os, Sb, Hv, Pe |
0.10 |
20.92 |
1.00 |
0.0032 |
None |
95L, 160T, 195V |
|
| GRMZM2G039639 |
Protein P21 |
31461924-se |
Zm, Si, Bd, Os, Sb, Ta, Hv, Pe |
0.80 |
179.11 |
1.00 |
0.0002 |
None |
23L, 34V, 98V, 107A, 145G, 161S, 165A, 202K, 209P |
|
| GRMZM2G080499 |
Hypothetical protein |
31455526-e |
Zm, Si, Bd, Os, Sb, Hv |
0.52 |
82.64 |
1.00 |
0.0001 |
None |
67T, 90T, 93T, 161P, 400S, 452T, 803V |
|
| GRMZM2G117971 |
Hypothetical protein LOC100191593 |
31462333-se |
Zm, Si, Bd, Os, Sb, Ta, Hv |
0.45 |
133.46 |
2.57 |
0.0001 |
None |
33Q, 36G, 50N, 103T, 108S, 118S, 131K, 138Q |
|
| GRMZM2G322129 |
Putative uncharacterized protein |
31457048 |
Zm, Si, Bd, Os, Sb |
0.85 |
189.35 |
1.00 |
1.6598 |
None |
28V, 37P, 38H, 119R, 135L, 172G, 173S, 203S, 228R, 250K, 255D, 263M, 284H, 312D, 434L, 595S |
|
| GRMZM2G057093 | Chitinase | 31480783 sec | Zm, Si, Bd, Os, Sb | 0.74 | 80.97 | 4.38 | 0.0614 | None | 177T, 277S | |
Cluster: clusters are named according to Phytozome v8.0 (Grass node), adding “e” when the cluster was expanded to other Poaceae species and “s” when a subtree was extracted from original Phytozome cluster. Species: one sequence for each of the following species was included in the cluster: Zm: Zea mays, Sb: Sorghum bicolor, Si: Setaria italica, Os: Oryza sativa, Bd: Brachypodium distachyon, Ta: Triticum aestivum, Hv: Hordeum vulgare, Pe: Phyllostachys edulis, As: Aegilops speltoides, Sc: Secale cereale, Or: Oryza rufipogon, Tm: Triticum monococcum. ω = dN/dS estimated under M3 and M8. Δ2L: likelihood ratio estimated as 2*(lnL1-lnL0) between M0vsM3 and M7vsM8, in bold those are statically significant at 0.05. PSS: Positively selected sites indentified by BEB when the approximate mean of the posterior distribution for w is > 1. Clusters with posterior probability > 0.8, * > 0.95 and ** > 0.99 are in bold type. PSS (MEME) show sites identified by MEME as under episodic selection (p-value < 0.1). In both cases amino acids refer to maize sequence.