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: ORTHO03M003360
Gene count gene family: 8
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	0	7.06%	0%	0
Oryza sativa ssp. japonica	40,738	1	8.1%	12.5%	1.54
Oryza sativa ssp. indica	49,202	0	9.78%	0%	0
Brachypodium distachyon	26,632	0	5.29%	0%	0
Hordeum vulgare	24,318	1	4.83%	12.5%	2.59
Musa acuminata	36,638	1	7.28%	12.5%	1.72
Arabidopsis thaliana	27,416	1	5.45%	12.5%	2.29
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	1	6.92%	12.5%	1.81
Physcomitrella patens	32,400	1	6.44%	12.5%	1.94
Ostreococcus lucimarinus	7,805	1	1.55%	12.5%	8.06
Chlamydomonas reinhardtii	17,819	1	3.54%	12.5%	3.53

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	0	21.76%	0%	0
Oryza	2	89,940	1	17.87%	12.5%	0.7
Pooideae	2	50,950	1	10.12%	12.5%	1.24
BEP_Clade	4	140,890	2	28%	25%	0.89
Poaceae	7	250,375	2	49.75%	25%	0.5
Monocots	8	287,013	3	57.03%	37.5%	0.66
Brassicales	2	55,443	1	11.02%	12.5%	1.13
Rosids1	3	96,877	1	19.25%	12.5%	0.65
Rosids	4	123,381	1	24.52%	12.5%	0.51
Dicots	5	158,194	2	31.44%	25%	0.8
Angiosperms	13	445,207	5	88.47%	62.5%	0.71
Embryophyta	14	477,607	6	94.91%	75%	0.79
Chlorophyta	2	25,624	2	5.09%	25%	4.91
Viridiplantae	16	503,231	8	100%	100%	1