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: ORTHO03D015606
Gene count gene family: 5
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	0	8.82%	0%	0
Picea sitchensis	20,434	0	2.7%	0%	0
Pinus pinaster	76,426	0	10.12%	0%	0
Pinus sylvestris	36,106	0	4.78%	0%	0
Pinus taeda	84,446	0	11.18%	0%	0
Pseudotsuga menziesii	149,717	0	19.82%	0%	0
Gnetum montanum	32,549	1	4.31%	20%	4.64
Taxus baccata	32,062	0	4.24%	0%	0
Cycas micholitzii	28,901	0	3.83%	0%	0
Ginkgo biloba	30,404	1	4.02%	20%	4.98
Populus trichocarpa	41,434	1	5.48%	20%	3.65
Arabidopsis thaliana	27,416	1	3.63%	20%	5.51
Oryza sativa ssp. japonica	40,738	0	5.39%	0%	0
Amborella trichopoda	26,931	1	3.56%	20%	5.62
Physcomitrella patens	32,400	0	4.29%	0%	0

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Picea	3	115,975	0	15.35%	0%	0
Pinus	3	196,978	0	26.07%	0%	0
Pinaceae	7	462,670	0	61.24%	0%	0
Gymnosperms	11	586,586	2	77.64%	40%	0.52
Angiosperms	4	136,519	3	18.07%	60%	3.32
Embryophyta	16	755,505	5	100%	100%	1