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: HOM03M009304
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	4	7.81%	57.14%	7.32
Sorghum bicolor	34,609	0	6.88%	0%	0
Setaria italica	35,553	1	7.06%	14.29%	2.02
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	1	5.57%	14.29%	2.57
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%	14.29%	2.07
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	4	14.69%	57.14%	3.89
Panicoideae	3	109,485	5	21.76%	71.43%	3.28
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	5	49.75%	71.43%	1.44
Monocots	8	287,013	5	57.03%	71.43%	1.25
Brassicales	2	55,443	1	11.02%	14.29%	1.3
Rosids1	3	96,877	1	19.25%	14.29%	0.74
Rosids	4	123,381	1	24.52%	14.29%	0.58
Dicots	5	158,194	2	31.44%	28.57%	0.91
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