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: ORTHO03M002253
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	1	9.78%	11.11%	1.14
Brachypodium distachyon	26,632	0	5.29%	0%	0
Hordeum vulgare	24,318	1	4.83%	11.11%	2.3
Musa acuminata	36,638	0	7.28%	0%	0
Arabidopsis thaliana	27,416	0	5.45%	0%	0
Carica papaya	28,027	0	5.57%	0%	0
Populus trichocarpa	41,434	2	8.23%	22.22%	2.7
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	1	6.92%	11.11%	1.61
Physcomitrella patens	32,400	0	6.44%	0%	0
Ostreococcus lucimarinus	7,805	0	1.55%	0%	0
Chlamydomonas reinhardtii	17,819	1	3.54%	11.11%	3.14

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	1	17.87%	11.11%	0.62
Pooideae	2	50,950	1	10.12%	11.11%	1.1
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	0	11.02%	0%	0
Rosids1	3	96,877	2	19.25%	22.22%	1.15
Rosids	4	123,381	2	24.52%	22.22%	0.91
Dicots	5	158,194	3	31.44%	33.33%	1.06
Angiosperms	13	445,207	8	88.47%	88.89%	1
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