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: HOM03D004471
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	1	3.83%	3.45%	0.9
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	2	10.12%	6.9%	0.68
Pinus sylvestris	36,106	2	4.78%	6.9%	1.44
Pinus taeda	84,446	2	11.18%	6.9%	0.62
Pseudotsuga menziesii	149,717	4	19.82%	13.79%	0.7
Gnetum montanum	32,549	2	4.31%	6.9%	1.6
Taxus baccata	32,062	2	4.24%	6.9%	1.63
Cycas micholitzii	28,901	1	3.83%	3.45%	0.9
Ginkgo biloba	30,404	4	4.02%	13.79%	3.43
Populus trichocarpa	41,434	2	5.48%	6.9%	1.26
Arabidopsis thaliana	27,416	0	3.63%	0%	0
Oryza sativa ssp. japonica	40,738	1	5.39%	3.45%	0.64
Amborella trichopoda	26,931	1	3.56%	3.45%	0.97
Physcomitrella patens	32,400	2	4.29%	6.9%	1.61

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%	13.79%	0.9
Pinus	3	196,978	6	26.07%	20.69%	0.79
Pinaceae	7	462,670	14	61.24%	48.28%	0.79
Gymnosperms	11	586,586	23	77.64%	79.31%	1.02
Angiosperms	4	136,519	4	18.07%	13.79%	0.76
Embryophyta	16	755,505	29	100%	100%	1