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: ORTHO03M002026
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	0	6.88%	0%	0
Setaria italica	35,553	0	7.06%	0%	0
Oryza sativa ssp. japonica	40,738	1	8.1%	11.11%	1.37
Oryza sativa ssp. indica	49,202	2	9.78%	22.22%	2.27
Brachypodium distachyon	26,632	1	5.29%	11.11%	2.1
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	1	7.28%	11.11%	1.53
Arabidopsis thaliana	27,416	0	5.45%	0%	0
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	0	6.92%	0%	0
Physcomitrella patens	32,400	3	6.44%	33.33%	5.18
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%	11.11%	0.76
Panicoideae	3	109,485	1	21.76%	11.11%	0.51
Oryza	2	89,940	3	17.87%	33.33%	1.87
Pooideae	2	50,950	1	10.12%	11.11%	1.1
BEP_Clade	4	140,890	4	28%	44.44%	1.59
Poaceae	7	250,375	5	49.75%	55.56%	1.12
Monocots	8	287,013	6	57.03%	66.67%	1.17
Brassicales	2	55,443	0	11.02%	0%	0
Rosids1	3	96,877	0	19.25%	0%	0
Rosids	4	123,381	0	24.52%	0%	0
Dicots	5	158,194	0	31.44%	0%	0
Angiosperms	13	445,207	6	88.47%	66.67%	0.75
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