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: ORTHO03M002003
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	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	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	2	7.28%	22.22%	3.05
Arabidopsis thaliana	27,416	1	5.45%	11.11%	2.04
Carica papaya	28,027	1	5.57%	11.11%	1.99
Populus trichocarpa	41,434	0	8.23%	0%	0
Vitis vinifera	26,504	1	5.27%	11.11%	2.11
Solanum lycopersicum	34,813	1	6.92%	11.11%	1.61
Physcomitrella patens	32,400	2	6.44%	22.22%	3.45
Ostreococcus lucimarinus	7,805	1	1.55%	11.11%	7.17
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	0	14.69%	0%	0
Panicoideae	3	109,485	0	21.76%	0%	0
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	0	49.75%	0%	0
Monocots	8	287,013	2	57.03%	22.22%	0.39
Brassicales	2	55,443	2	11.02%	22.22%	2.02
Rosids1	3	96,877	2	19.25%	22.22%	1.15
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	6	88.47%	66.67%	0.75
Embryophyta	14	477,607	8	94.91%	88.89%	0.94
Chlorophyta	2	25,624	1	5.09%	11.11%	2.18
Viridiplantae	16	503,231	9	100%	100%	1