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: ORTHO03M004001
Gene count gene family: 7
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	0	7.06%	0%	0
Oryza sativa ssp. japonica	40,738	1	8.1%	14.29%	1.76
Oryza sativa ssp. indica	49,202	1	9.78%	14.29%	1.46
Brachypodium distachyon	26,632	0	5.29%	0%	0
Hordeum vulgare	24,318	0	4.83%	0%	0
Musa acuminata	36,638	2	7.28%	28.57%	3.92
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	2	6.92%	28.57%	4.13
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%	14.29%	4.04

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	0	21.76%	0%	0
Oryza	2	89,940	2	17.87%	28.57%	1.6
Pooideae	2	50,950	0	10.12%	0%	0
BEP_Clade	4	140,890	2	28%	28.57%	1.02
Poaceae	7	250,375	2	49.75%	28.57%	0.57
Monocots	8	287,013	4	57.03%	57.14%	1
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	2	31.44%	28.57%	0.91
Angiosperms	13	445,207	6	88.47%	85.71%	0.97
Embryophyta	14	477,607	6	94.91%	85.71%	0.9
Chlorophyta	2	25,624	1	5.09%	14.29%	2.81
Viridiplantae	16	503,231	7	100%	100%	1