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: ORTHO03M003123
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	0	7.81%	0%	0
Sorghum bicolor	34,609	0	6.88%	0%	0
Setaria italica	35,553	2	7.06%	25%	3.54
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	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	3	8.23%	37.5%	4.56
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	3	6.92%	37.5%	5.42
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	0	14.69%	0%	0
Panicoideae	3	109,485	2	21.76%	25%	1.15
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	2	49.75%	25%	0.5
Monocots	8	287,013	2	57.03%	25%	0.44
Brassicales	2	55,443	0	11.02%	0%	0
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	6	31.44%	75%	2.39
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