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: ORTHO03M003595
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	1	6.88%	12.5%	1.82
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	1	5.29%	12.5%	2.36
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	0	5.45%	0%	0
Carica papaya	28,027	1	5.57%	12.5%	2.24
Populus trichocarpa	41,434	1	8.23%	12.5%	1.52
Vitis vinifera	26,504	1	5.27%	12.5%	2.37
Solanum lycopersicum	34,813	0	6.92%	0%	0
Physcomitrella patens	32,400	0	6.44%	0%	0
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%	12.5%	0.85
Panicoideae	3	109,485	1	21.76%	12.5%	0.57
Oryza	2	89,940	1	17.87%	12.5%	0.7
Pooideae	2	50,950	2	10.12%	25%	2.47
BEP_Clade	4	140,890	3	28%	37.5%	1.34
Poaceae	7	250,375	4	49.75%	50%	1.01
Monocots	8	287,013	5	57.03%	62.5%	1.1
Brassicales	2	55,443	1	11.02%	12.5%	1.13
Rosids1	3	96,877	2	19.25%	25%	1.3
Rosids	4	123,381	3	24.52%	37.5%	1.53
Dicots	5	158,194	3	31.44%	37.5%	1.19
Angiosperms	13	445,207	8	88.47%	100%	1.13
Embryophyta	14	477,607	8	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	8	100%	100%	1