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: ORTHO03M006804
Gene count gene family: 6
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	1	7.06%	16.67%	2.36
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%	16.67%	3.15
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	1	7.28%	16.67%	2.29
Arabidopsis thaliana	27,416	0	5.45%	0%	0
Carica papaya	28,027	0	5.57%	0%	0
Populus trichocarpa	41,434	1	8.23%	16.67%	2.03
Vitis vinifera	26,504	1	5.27%	16.67%	3.16
Solanum lycopersicum	34,813	0	6.92%	0%	0
Physcomitrella patens	32,400	1	6.44%	16.67%	2.59
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	1	21.76%	16.67%	0.77
Oryza	2	89,940	0	17.87%	0%	0
Pooideae	2	50,950	1	10.12%	16.67%	1.65
BEP_Clade	4	140,890	1	28%	16.67%	0.6
Poaceae	7	250,375	2	49.75%	33.33%	0.67
Monocots	8	287,013	3	57.03%	50%	0.88
Brassicales	2	55,443	0	11.02%	0%	0
Rosids1	3	96,877	1	19.25%	16.67%	0.87
Rosids	4	123,381	2	24.52%	33.33%	1.36
Dicots	5	158,194	2	31.44%	33.33%	1.06
Angiosperms	13	445,207	5	88.47%	83.33%	0.94
Embryophyta	14	477,607	6	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	6	100%	100%	1