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: ORTHO03M002145
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	1	7.81%	11.11%	1.42
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	1	7.28%	11.11%	1.53
Arabidopsis thaliana	27,416	0	5.45%	0%	0
Carica papaya	28,027	1	5.57%	11.11%	1.99
Populus trichocarpa	41,434	2	8.23%	22.22%	2.7
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	1	6.92%	11.11%	1.61
Physcomitrella patens	32,400	1	6.44%	11.11%	1.73
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	1	14.69%	11.11%	0.76
Panicoideae	3	109,485	2	21.76%	22.22%	1.02
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	3	49.75%	33.33%	0.67
Monocots	8	287,013	4	57.03%	44.44%	0.78
Brassicales	2	55,443	1	11.02%	11.11%	1.01
Rosids1	3	96,877	3	19.25%	33.33%	1.73
Rosids	4	123,381	3	24.52%	33.33%	1.36
Dicots	5	158,194	4	31.44%	44.44%	1.41
Angiosperms	13	445,207	8	88.47%	88.89%	1
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