PLAZA 3.0 Dicots : 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: ORTHO03D017965
Gene count gene family: 8
Total coding gene count: 1,012,693

Keywords

Organisms

Organism	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Arabidopsis thaliana	27,416	0	2.71%	0%	0
Arabidopsis lyrata	32,670	0	3.23%	0%	0
Capsella rubella	26,521	0	2.62%	0%	0
Brassica rapa	40,977	0	4.05%	0%	0
Thellungiella parvula	25,691	0	2.54%	0%	0
Carica papaya	28,027	0	2.77%	0%	0
Gossypium raimondii	37,587	0	3.71%	0%	0
Theobroma cacao	29,484	0	2.91%	0%	0
Citrus sinensis	25,467	0	2.51%	0%	0
Eucalyptus grandis	36,449	0	3.6%	0%	0
Cucumis melo	27,514	0	2.72%	0%	0
Citrullus lanatus	23,477	0	2.32%	0%	0
Prunus persica	27,864	0	2.75%	0%	0
Malus domestica	63,546	0	6.27%	0%	0
Fragaria vesca	34,809	0	3.44%	0%	0
Lotus japonicus	29,598	0	2.92%	0%	0
Medicago truncatula	50,893	1	5.03%	12.5%	2.49
Glycine max	54,257	0	5.36%	0%	0
Ricinus communis	31,221	0	3.08%	0%	0
Manihot esculenta	30,748	0	3.04%	0%	0
Populus trichocarpa	41,434	0	4.09%	0%	0
Vitis vinifera	26,504	0	2.62%	0%	0
Solanum lycopersicum	34,813	1	3.44%	12.5%	3.63
Solanum tuberosum	35,085	0	3.46%	0%	0
Beta vulgaris	25,625	0	2.53%	0%	0
Zea mays	39,323	0	3.88%	0%	0
Oryza sativa ssp. japonica	40,738	0	4.02%	0%	0
Amborella trichopoda	26,931	0	2.66%	0%	0
Physcomitrella patens	32,400	6	3.2%	75%	23.44
Ostreococcus lucimarinus	7,805	0	0.77%	0%	0
Chlamydomonas reinhardtii	17,819	0	1.76%	0%	0

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Arabidopsis	2	60,086	0	5.93%	0%	0
Camelineae	3	86,607	0	8.55%	0%	0
ND_Brassicaceae1	2	66,668	0	6.58%	0%	0
Brassicaceae	5	153,275	0	15.14%	0%	0
Brassicales	6	181,302	0	17.9%	0%	0
Malvales	2	67,071	0	6.62%	0%	0
ND_Malvids1	8	248,373	0	24.53%	0%	0
ND_Malvids2	9	273,840	0	27.04%	0%	0
Malvids	10	310,289	0	30.64%	0%	0
Benincaseae	2	50,991	0	5.04%	0%	0
Maloideae	2	91,410	0	9.03%	0%	0
Rosaceae	3	126,219	0	12.46%	0%	0
ND_Fabids1	5	177,210	0	17.5%	0%	0
Galegoids	2	80,491	1	7.95%	12.5%	1.57
Papilionoideae	3	134,748	1	13.31%	12.5%	0.94
ND_Fabids2	8	311,958	1	30.8%	12.5%	0.41
Euphorbiaceae	2	61,969	0	6.12%	0%	0
Malpighiales	3	103,403	0	10.21%	0%	0
Fabids	11	415,361	1	41.02%	12.5%	0.3
Rosids1	21	725,650	1	71.66%	12.5%	0.17
Rosids	22	752,154	1	74.27%	12.5%	0.17
Solanum	2	69,898	1	6.9%	12.5%	1.81
ND_Dicots	24	822,052	2	81.17%	25%	0.31
Dicots	25	847,677	2	83.71%	25%	0.3
Monocots	2	80,061	0	7.91%	0%	0
Angiosperms	27	927,738	2	91.61%	25%	0.27
Magnoliophyta	28	954,669	2	94.27%	25%	0.27
Embryophyta	29	987,069	8	97.47%	100%	1.03
Chlorophyta	2	25,624	0	2.53%	0%	0
Viridiplantae	31	1,012,693	8	100%	100%	1