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: ORTHO03M008666
Gene count gene family: 5
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%	20%	2.56
Sorghum bicolor	34,609	1	6.88%	20%	2.91
Setaria italica	35,553	0	7.06%	0%	0
Oryza sativa ssp. japonica	40,738	0	8.1%	0%	0
Oryza sativa ssp. indica	49,202	0	9.78%	0%	0
Brachypodium distachyon	26,632	0	5.29%	0%	0
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	0	7.28%	0%	0
Arabidopsis thaliana	27,416	1	5.45%	20%	3.67
Carica papaya	28,027	0	5.57%	0%	0
Populus trichocarpa	41,434	0	8.23%	0%	0
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	0	6.92%	0%	0
Physcomitrella patens	32,400	0	6.44%	0%	0
Ostreococcus lucimarinus	7,805	1	1.55%	20%	12.9
Chlamydomonas reinhardtii	17,819	1	3.54%	20%	5.65

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Andropogoneae	2	73,932	2	14.69%	40%	2.72
Panicoideae	3	109,485	2	21.76%	40%	1.84
Oryza	2	89,940	0	17.87%	0%	0
Pooideae	2	50,950	0	10.12%	0%	0
BEP_Clade	4	140,890	0	28%	0%	0
Poaceae	7	250,375	2	49.75%	40%	0.8
Monocots	8	287,013	2	57.03%	40%	0.7
Brassicales	2	55,443	1	11.02%	20%	1.81
Rosids1	3	96,877	1	19.25%	20%	1.04
Rosids	4	123,381	1	24.52%	20%	0.82
Dicots	5	158,194	1	31.44%	20%	0.64
Angiosperms	13	445,207	3	88.47%	60%	0.68
Embryophyta	14	477,607	3	94.91%	60%	0.63
Chlorophyta	2	25,624	2	5.09%	40%	7.86
Viridiplantae	16	503,231	5	100%	100%	1