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: ORTHO03M003963
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	2	4.83%	28.57%	5.92
Musa acuminata	36,638	0	7.28%	0%	0
Arabidopsis thaliana	27,416	1	5.45%	14.29%	2.62
Carica papaya	28,027	0	5.57%	0%	0
Populus trichocarpa	41,434	2	8.23%	28.57%	3.47
Vitis vinifera	26,504	0	5.27%	0%	0
Solanum lycopersicum	34,813	0	6.92%	0%	0
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	0	21.76%	0%	0
Oryza	2	89,940	2	17.87%	28.57%	1.6
Pooideae	2	50,950	2	10.12%	28.57%	2.82
BEP_Clade	4	140,890	4	28%	57.14%	2.04
Poaceae	7	250,375	4	49.75%	57.14%	1.15
Monocots	8	287,013	4	57.03%	57.14%	1
Brassicales	2	55,443	1	11.02%	14.29%	1.3
Rosids1	3	96,877	3	19.25%	42.86%	2.23
Rosids	4	123,381	3	24.52%	42.86%	1.75
Dicots	5	158,194	3	31.44%	42.86%	1.36
Angiosperms	13	445,207	7	88.47%	100%	1.13
Embryophyta	14	477,607	7	94.91%	100%	1.05
Chlorophyta	2	25,624	0	5.09%	0%	0
Viridiplantae	16	503,231	7	100%	100%	1