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: ORTHO03M008407
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	0	6.88%	0%	0
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	1	5.29%	20%	3.78
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	1	7.28%	20%	2.75
Arabidopsis thaliana	27,416	1	5.45%	20%	3.67
Carica papaya	28,027	1	5.57%	20%	3.59
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	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%	20%	1.36
Panicoideae	3	109,485	1	21.76%	20%	0.92
Oryza	2	89,940	0	17.87%	0%	0
Pooideae	2	50,950	1	10.12%	20%	1.98
BEP_Clade	4	140,890	1	28%	20%	0.71
Poaceae	7	250,375	2	49.75%	40%	0.8
Monocots	8	287,013	3	57.03%	60%	1.05
Brassicales	2	55,443	2	11.02%	40%	3.63
Rosids1	3	96,877	2	19.25%	40%	2.08
Rosids	4	123,381	2	24.52%	40%	1.63
Dicots	5	158,194	2	31.44%	40%	1.27
Angiosperms	13	445,207	5	88.47%	100%	1.13
Embryophyta	14	477,607	5	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	5	100%	100%	1