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: ORTHO03M002410
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	1	7.81%	11.11%	1.42
Sorghum bicolor	34,609	1	6.88%	11.11%	1.61
Setaria italica	35,553	1	7.06%	11.11%	1.57
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%	11.11%	2.1
Hordeum vulgare	24,318	1	4.83%	11.11%	2.3
Musa acuminata	36,638	0	7.28%	0%	0
Arabidopsis thaliana	27,416	1	5.45%	11.11%	2.04
Carica papaya	28,027	2	5.57%	22.22%	3.99
Populus trichocarpa	41,434	0	8.23%	0%	0
Vitis vinifera	26,504	1	5.27%	11.11%	2.11
Solanum lycopersicum	34,813	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	2	14.69%	22.22%	1.51
Panicoideae	3	109,485	3	21.76%	33.33%	1.53
Oryza	2	89,940	0	17.87%	0%	0
Pooideae	2	50,950	2	10.12%	22.22%	2.2
BEP_Clade	4	140,890	2	28%	22.22%	0.79
Poaceae	7	250,375	5	49.75%	55.56%	1.12
Monocots	8	287,013	5	57.03%	55.56%	0.97
Brassicales	2	55,443	3	11.02%	33.33%	3.02
Rosids1	3	96,877	3	19.25%	33.33%	1.73
Rosids	4	123,381	4	24.52%	44.44%	1.81
Dicots	5	158,194	4	31.44%	44.44%	1.41
Angiosperms	13	445,207	9	88.47%	100%	1.13
Embryophyta	14	477,607	9	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	9	100%	100%	1