PLAZA Gymnosperms : 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: HOM03D004487
Gene count gene family: 29
Total coding gene count: 755,505

Keywords

Organisms

Organism	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Picea glauca	28,909	0	3.83%	0%	0
Picea abies	66,632	2	8.82%	6.9%	0.78
Picea sitchensis	20,434	1	2.7%	3.45%	1.28
Pinus pinaster	76,426	6	10.12%	20.69%	2.04
Pinus sylvestris	36,106	1	4.78%	3.45%	0.72
Pinus taeda	84,446	2	11.18%	6.9%	0.62
Pseudotsuga menziesii	149,717	6	19.82%	20.69%	1.04
Gnetum montanum	32,549	1	4.31%	3.45%	0.8
Taxus baccata	32,062	1	4.24%	3.45%	0.81
Cycas micholitzii	28,901	1	3.83%	3.45%	0.9
Ginkgo biloba	30,404	1	4.02%	3.45%	0.86
Populus trichocarpa	41,434	2	5.48%	6.9%	1.26
Arabidopsis thaliana	27,416	1	3.63%	3.45%	0.95
Oryza sativa ssp. japonica	40,738	1	5.39%	3.45%	0.64
Amborella trichopoda	26,931	2	3.56%	6.9%	1.94
Physcomitrella patens	32,400	1	4.29%	3.45%	0.8

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Picea	3	115,975	3	15.35%	10.34%	0.67
Pinus	3	196,978	9	26.07%	31.03%	1.19
Pinaceae	7	462,670	18	61.24%	62.07%	1.01
Gymnosperms	11	586,586	22	77.64%	75.86%	0.98
Angiosperms	4	136,519	6	18.07%	20.69%	1.14
Embryophyta	16	755,505	29	100%	100%	1