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: ORTHO03M002680
Gene count gene family: 8
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%	12.5%	1.6
Sorghum bicolor	34,609	0	6.88%	0%	0
Setaria italica	35,553	0	7.06%	0%	0
Oryza sativa ssp. japonica	40,738	2	8.1%	25%	3.09
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	0	7.28%	0%	0
Arabidopsis thaliana	27,416	1	5.45%	12.5%	2.29
Carica papaya	28,027	1	5.57%	12.5%	2.24
Populus trichocarpa	41,434	1	8.23%	12.5%	1.52
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	2	6.92%	25%	3.61
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%	12.5%	0.85
Panicoideae	3	109,485	1	21.76%	12.5%	0.57
Oryza	2	89,940	2	17.87%	25%	1.4
Pooideae	2	50,950	0	10.12%	0%	0
BEP_Clade	4	140,890	2	28%	25%	0.89
Poaceae	7	250,375	3	49.75%	37.5%	0.75
Monocots	8	287,013	3	57.03%	37.5%	0.66
Brassicales	2	55,443	2	11.02%	25%	2.27
Rosids1	3	96,877	3	19.25%	37.5%	1.95
Rosids	4	123,381	3	24.52%	37.5%	1.53
Dicots	5	158,194	5	31.44%	62.5%	1.99
Angiosperms	13	445,207	8	88.47%	100%	1.13
Embryophyta	14	477,607	8	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	8	100%	100%	1