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: HOM03D007699
Gene count gene family: 16
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	1	3.83%	6.25%	1.63
Picea abies	66,632	1	8.82%	6.25%	0.71
Picea sitchensis	20,434	2	2.7%	12.5%	4.63
Pinus pinaster	76,426	2	10.12%	12.5%	1.24
Pinus sylvestris	36,106	1	4.78%	6.25%	1.31
Pinus taeda	84,446	0	11.18%	0%	0
Pseudotsuga menziesii	149,717	1	19.82%	6.25%	0.32
Gnetum montanum	32,549	1	4.31%	6.25%	1.45
Taxus baccata	32,062	0	4.24%	0%	0
Cycas micholitzii	28,901	1	3.83%	6.25%	1.63
Ginkgo biloba	30,404	2	4.02%	12.5%	3.11
Populus trichocarpa	41,434	1	5.48%	6.25%	1.14
Arabidopsis thaliana	27,416	1	3.63%	6.25%	1.72
Oryza sativa ssp. japonica	40,738	1	5.39%	6.25%	1.16
Amborella trichopoda	26,931	0	3.56%	0%	0
Physcomitrella patens	32,400	1	4.29%	6.25%	1.46

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Picea	3	115,975	4	15.35%	25%	1.63
Pinus	3	196,978	3	26.07%	18.75%	0.72
Pinaceae	7	462,670	8	61.24%	50%	0.82
Gymnosperms	11	586,586	12	77.64%	75%	0.97
Angiosperms	4	136,519	3	18.07%	18.75%	1.04
Embryophyta	16	755,505	16	100%	100%	1