PLAZA 3.0 Monocots : Gene family expansion analysis

Gene family expansion analysis

Tool which reports the expansion/depletion of a species/lineage (through gene copy number variation compared to total proteome sizes of the species) within a gene family.

Gene family: ORTHO03M001916
Gene count gene family: 9
Total coding gene count: 503,231

Keywords

Organisms

Organism	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Zea mays	39,323	0	7.81%	0%	0
Sorghum bicolor	34,609	0	6.88%	0%	0
Setaria italica	35,553	1	7.06%	11.11%	1.57
Oryza sativa ssp. japonica	40,738	0	8.1%	0%	0
Oryza sativa ssp. indica	49,202	1	9.78%	11.11%	1.14
Brachypodium distachyon	26,632	0	5.29%	0%	0
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	3	7.28%	33.33%	4.58
Arabidopsis thaliana	27,416	0	5.45%	0%	0
Carica papaya	28,027	1	5.57%	11.11%	1.99
Populus trichocarpa	41,434	1	8.23%	11.11%	1.35
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	0	6.92%	0%	0
Physcomitrella patens	32,400	2	6.44%	22.22%	3.45
Ostreococcus lucimarinus	7,805	0	1.55%	0%	0
Chlamydomonas reinhardtii	17,819	0	3.54%	0%	0

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Andropogoneae	2	73,932	0	14.69%	0%	0
Panicoideae	3	109,485	1	21.76%	11.11%	0.51
Oryza	2	89,940	1	17.87%	11.11%	0.62
Pooideae	2	50,950	0	10.12%	0%	0
BEP_Clade	4	140,890	1	28%	11.11%	0.4
Poaceae	7	250,375	2	49.75%	22.22%	0.45
Monocots	8	287,013	5	57.03%	55.56%	0.97
Brassicales	2	55,443	1	11.02%	11.11%	1.01
Rosids1	3	96,877	2	19.25%	22.22%	1.15
Rosids	4	123,381	2	24.52%	22.22%	0.91
Dicots	5	158,194	2	31.44%	22.22%	0.71
Angiosperms	13	445,207	7	88.47%	77.78%	0.88
Embryophyta	14	477,607	9	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	9	100%	100%	1