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: ORTHO03M010838
Gene count gene family: 4
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%	25%	3.2
Sorghum bicolor	34,609	0	6.88%	0%	0
Setaria italica	35,553	2	7.06%	50%	7.08
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	0	8.23%	0%	0
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	1	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%	25%	1.7
Panicoideae	3	109,485	3	21.76%	75%	3.45
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	3	49.75%	75%	1.51
Monocots	8	287,013	3	57.03%	75%	1.32
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	1	31.44%	25%	0.8
Angiosperms	13	445,207	4	88.47%	100%	1.13
Embryophyta	14	477,607	4	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	4	100%	100%	1