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. 2012 Dec 1;7(12):1667–1675. doi: 10.4161/psb.22362

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.